From 847acc3206c34b45cabd4f5ae1465a576d7ef10a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 29 Mar 2022 13:42:48 +0200 Subject: gnu: pigx-rnaseq: Update to 0.0.20. * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.20. [source]: Remove patch. [inputs]: Add megadepth. * gnu/packages/patches/pigx-rnaseq-no-citeproc.patch: Remove patch. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/packages/bioinformatics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ada5965e5f..c42174e0d6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10869,7 +10869,7 @@ once. This package provides tools to perform Drop-seq analyses.") (define-public pigx-rnaseq (package (name "pigx-rnaseq") - (version "0.0.19") + (version "0.0.20") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/" @@ -10877,8 +10877,7 @@ once. This package provides tools to perform Drop-seq analyses.") "/pigx_rnaseq-" version ".tar.gz")) (sha256 (base32 - "1ja3bda1appxrzbfy7wp7khy30mm7lic8xbq3gkbpc5bld3as9cm")) - (patches (search-patches "pigx-rnaseq-no-citeproc.patch")))) + "0bf65qqvlkc77vl7cmmzacq70f0qav4p6nf8pp3x1vdd0nvhr24f")))) (build-system gnu-build-system) (arguments `(#:parallel-tests? #f ; not supported @@ -10909,6 +10908,7 @@ once. This package provides tools to perform Drop-seq analyses.") sed gzip snakemake + megadepth multiqc star-for-pigx hisat2 -- cgit v1.2.3 From 6d5964e8049b141b447c020e699ecaddc29e28fd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 29 Mar 2022 13:49:50 +0200 Subject: gnu: pigx-sars-cov2-ww: Update to 0.0.5. * gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.5. [source]: Remove patch. [arguments]: Disable tests. * gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/bioinformatics.scm | 8 +++--- .../patches/pigx-sars-cov2-ww-no-citeproc.patch | 33 ---------------------- 3 files changed, 4 insertions(+), 38 deletions(-) delete mode 100644 gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/local.mk b/gnu/local.mk index 3f4f2c187d..a704161abc 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1628,7 +1628,6 @@ dist_patch_DATA = \ %D%/packages/patches/pidgin-add-search-path.patch \ %D%/packages/patches/pigx-bsseq-no-citeproc.patch \ %D%/packages/patches/pigx-chipseq-no-citeproc.patch \ - %D%/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch \ %D%/packages/patches/pigx-scrnaseq-no-citeproc.patch \ %D%/packages/patches/pinball-system-ltdl.patch \ %D%/packages/patches/pingus-boost-headers.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c42174e0d6..73b9ee6da8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11192,7 +11192,7 @@ based methods.") (define-public pigx-sars-cov2-ww (package (name "pigx-sars-cov2-ww") - (version "0.0.4") + (version "0.0.5") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_sarscov2_ww/" @@ -11200,11 +11200,11 @@ based methods.") "/pigx_sars-cov2-ww-" version ".tar.gz")) (sha256 (base32 - "0axnmz4d8zgir888mc0cilcq4m3v41xmjmpp3w3444lciwnxydvs")) - (patches (search-patches "pigx-sars-cov2-ww-no-citeproc.patch")))) + "1fkr9gp09zl5n7kdqmy9lrnq28k2z97wg74wgkyfssfyxvmq9cr2")))) (build-system gnu-build-system) (arguments - `(#:phases + `(#:tests? #f ;requires huge kraken database + #:phases (modify-phases %standard-phases (add-before 'bootstrap 'autoreconf (lambda _ diff --git a/gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch b/gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch deleted file mode 100644 index 3f34bca6b2..0000000000 --- a/gnu/packages/patches/pigx-sars-cov2-ww-no-citeproc.patch +++ /dev/null @@ -1,33 +0,0 @@ -diff -Naur pigx_sars-cov2-ww-0.0.3/configure.ac pigx_sars-cov2-ww-0.0.3.patched/configure.ac ---- pigx_sars-cov2-ww-0.0.3/configure.ac 2021-06-10 10:12:00.552889984 +0200 -+++ pigx_sars-cov2-ww-0.0.3.patched/configure.ac 2021-10-05 14:52:32.318695129 +0200 -@@ -50,7 +50,6 @@ - find_or_override_prog([MULTIQC], [multiqc]) - find_or_override_prog([WGET], [wget]) - find_or_override_prog([PANDOC], [pandoc]) --find_or_override_prog([PANDOC_CITEPROC], [pandoc-citeproc]) - - AC_ARG_ENABLE([r-packages-check], - AS_HELP_STRING([--disable-r-packages-check], [Do not check any R packages.]), -diff -Naur pigx_sars-cov2-ww-0.0.3/Makefile.in pigx_sars-cov2-ww-0.0.3.patched/Makefile.in ---- pigx_sars-cov2-ww-0.0.3/Makefile.in 2021-08-05 16:33:59.164123383 +0200 -+++ pigx_sars-cov2-ww-0.0.3.patched/Makefile.in 2021-10-05 14:52:41.272958547 +0200 -@@ -402,7 +402,6 @@ - PACKAGE_URL = @PACKAGE_URL@ - PACKAGE_VERSION = @PACKAGE_VERSION@ - PANDOC = @PANDOC@ --PANDOC_CITEPROC = @PANDOC_CITEPROC@ - PATH_SEPARATOR = @PATH_SEPARATOR@ - PRINSEQ = @PRINSEQ@ - PYTHON = @PYTHON@ -diff -Naur pigx_sars-cov2-ww-0.0.3/pigx-common/common/pigx-runner.in pigx_sars-cov2-ww-0.0.3.patched/pigx-common/common/pigx-runner.in ---- pigx_sars-cov2-ww-0.0.3/pigx-common/common/pigx-runner.in 2021-07-30 11:10:17.913115902 +0200 -+++ pigx_sars-cov2-ww-0.0.3.patched/pigx-common/common/pigx-runner.in 2021-10-05 14:52:23.602438714 +0200 -@@ -379,7 +379,6 @@ - if path.exists(bin): shutil.rmtree(bin) - os.makedirs(bin, exist_ok=True) - os.symlink('@PANDOC@', path.join(bin, "pandoc")) -- os.symlink('@PANDOC_CITEPROC@', path.join(bin, "pandoc-citeproc")) - os.symlink('@RSCRIPT@', path.join(bin, "Rscript")) - os.environ['PATH'] = path.abspath(bin) + ":" + os.environ['PATH'] - os.environ['PIGX_PATH'] = path.abspath(bin) + ":" + os.environ['PATH'] -- cgit v1.2.3 From d710f0195771a48a8c8c22f8da09bdac48efa951 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Tue, 22 Mar 2022 11:34:31 +0100 Subject: gnu: Add r-cytobackbone. * gnu/packages/bioinformatics.scm (r-cytobackbone): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioinformatics.scm | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 73b9ee6da8..590ada92f9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11813,6 +11813,47 @@ distributions. Homotypic doublet proportion estimation is achieved by finding the sum of squared cell annotation frequencies.") (license license:cc0)))) +;; There have been no releases. +(define-public r-cytobackbone + (let ((commit "4c1a0a35cc5ae1f8f516127cec92351d96fe26e7") + (revision "1")) + (package + (name "r-cytobackbone") + (version (git-version "1.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tchitchek-lab/CytoBackBone") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ahiad14zcgdk42xzw5xryic2ibn2l8lkrcdvl2b5sz2js028yb3")))) + (properties `((upstream-name . "CytoBackBone"))) + (build-system r-build-system) + (propagated-inputs + (list r-flowcore + r-flowutils + r-fnn + r-ggplot2 + r-preprocesscore)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/tchitchek-lab/CytoBackBone") + (synopsis "Merge phenotype information from different cytometric profiles") + (description + "This package implements an algorithm which increases the number of +simultaneously measurable markers and in this way helps with study of the +immune responses. Thus, the present algorithm, named @code{CytoBackBone}, +allows combining phenotypic information of cells from different cytometric +profiles obtained from different cytometry panels. This computational +approach is based on the principle that each cell has its own phenotypic and +functional characteristics that can be used as an identification card. +@code{CytoBackBone} uses a set of predefined markers, that we call the +backbone, to define this identification card. The phenotypic information of +cells with similar identification cards in the different cytometric profiles +is then merged.") + (license license:gpl2)))) + (define-public gffread ;; We cannot use the tagged release because it is not in sync with gclib. ;; See https://github.com/gpertea/gffread/issues/26 -- cgit v1.2.3 From 977a33139e7a3130c20a222772b845baa1fcbce4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 29 Mar 2022 15:33:55 +0200 Subject: gnu: plink-ng: Update to 2.00a3-20220315. * gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a3-20220315. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 590ada92f9..a2c9e1a37d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6668,7 +6668,7 @@ subsequent visualization, annotation and storage of results.") (define-public plink-ng (package (inherit plink) (name "plink-ng") - (version "2.00a2.3") + (version "2.00a3-20220315") (source (origin (method git-fetch) @@ -6677,7 +6677,7 @@ subsequent visualization, annotation and storage of results.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1p88lz9agzjlspjhciz61qjc36cfniv4nkxszyy0njqyc5rzc0cd")))) + (base32 "19inr47jwddkjb9kfb14yxc7xb16c73lkhgxj9sncb0fsiskb4x8")))) (build-system gnu-build-system) (arguments `(#:make-flags -- cgit v1.2.3 From 591007f7d12d598fe0eda698da07e79b180d1946 Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Wed, 23 Mar 2022 11:24:08 +0100 Subject: gnu: r-signac: Update to 1.6.0-2.458e647. * gnu/packages/bioinformatics.scm (r-signac): Update to 1.6.0-2.458e647. [propagated-inputs]: Remove r-annotationfilter, r-biocgenerics, r-biostrings, r-biovizbase, and r-ggbio; add r-qlcmatrix and r-tidyselect. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioinformatics.scm | 19 ++++++++----------- 1 file changed, 8 insertions(+), 11 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a2c9e1a37d..4e1028b3ce 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15316,11 +15316,11 @@ translates between different variant encodings.") (license license:asl2.0)))) (define-public r-signac - (let ((commit "e0512d348adeda4a3f23a2e8f56d1fe09840e03c") - (revision "1")) + (let ((commit "458e647b503c3472b0b98c0aeca934f452e039ee") + (revision "2")) (package (name "r-signac") - (version (git-version "1.1.1" revision commit)) + (version (git-version "1.6.0" revision commit)) (source (origin (method git-fetch) @@ -15329,16 +15329,12 @@ translates between different variant encodings.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 - "1yihhrv7zs87ax61la1nb4y12lg3knraw4b20k5digbcwm8488lb")))) + (base32 "1hgwpgighkvfkai80n4d2252s4sdpa4faag4ncdiylicl5wa7lbj")))) (properties `((upstream-name . "Signac"))) (build-system r-build-system) (inputs (list zlib)) (propagated-inputs - (list r-annotationfilter - r-biocgenerics - r-biostrings - r-biovizbase + (list r-biocgenerics r-data-table r-dplyr r-fastmatch @@ -15346,7 +15342,6 @@ translates between different variant encodings.") r-future-apply r-genomeinfodb r-genomicranges - r-ggbio r-ggforce r-ggplot2 r-ggrepel @@ -15357,6 +15352,7 @@ translates between different variant encodings.") r-matrix r-patchwork r-pbapply + r-qlcmatrix r-rcpp r-rcpproll r-rsamtools @@ -15365,7 +15361,8 @@ translates between different variant encodings.") r-seurat r-seuratobject r-stringi - r-tidyr)) + r-tidyr + r-tidyselect)) (home-page "https://github.com/timoast/signac/") (synopsis "Analysis of single-cell chromatin data") (description -- cgit v1.2.3 From a69a44bf598301cee2b74c46a49301efc0b3be3f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 31 Mar 2022 14:35:41 +0200 Subject: gnu: python-loompy: Update to 3.0.7. * gnu/packages/bioinformatics.scm (python-loompy): Update to 3.0.7. [arguments]: Add build phases 'fix-h5py-error and 'set-numba-cache-dir; respect TESTS? argument in 'check phase. [propagated-inputs]: Add python-click, python-numba, and python-numpy-groupies. --- gnu/packages/bioinformatics.scm | 27 ++++++++++++++++++++++----- 1 file changed, 22 insertions(+), 5 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4e1028b3ce..693158798a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10266,7 +10266,7 @@ variational inference.") (define-public python-loompy (package (name "python-loompy") - (version "2.0.17") + (version "3.0.7") ;; The tarball on Pypi does not include the tests. (source (origin (method git-fetch) @@ -10276,16 +10276,33 @@ variational inference.") (file-name (git-file-name name version)) (sha256 (base32 - "12a5kjgiikapv93wahfw0frszx1lblnppyz3vs5gy8fgmgngra07")))) + "0xmw2yv1y3y7vh5jcbrmlkn43nmfs0pf6z78k1yxqs3qy248m9b0")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases - (replace 'check + ;; See https://github.com/linnarsson-lab/loompy/issues/169 + (add-after 'unpack 'fix-h5py-error + (lambda _ + (substitute* "tests/test_file_attribute_manager.py" + (("h5py.File\\(f.name\\)") + "h5py.File(f.name, 'a')")))) + ;; Numba needs a writable dir to cache functions. + (add-before 'check 'set-numba-cache-dir (lambda _ - (invoke "pytest" "tests")))))) + (setenv "NUMBA_CACHE_DIR" "/tmp"))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "tests"))))))) (propagated-inputs - (list python-h5py python-numpy python-pandas python-scipy)) + (list python-click + python-h5py + python-numba + python-numpy + python-numpy-groupies + python-pandas + python-scipy)) (native-inputs (list python-pytest)) (home-page "https://github.com/linnarsson-lab/loompy") -- cgit v1.2.3 From 7d331dd20302ca1d7df4fc67bfcedde9d897cc97 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Thu, 31 Mar 2022 12:58:46 +0530 Subject: gnu: htslib: Add bzip2 and xz to inputs. htslib links to libbz2 from bzip2 and liblzma from xz. Therefore, bzip2 and xz should be listed in inputs even though they are already present implicitly in native-inputs. Else, cross-compilation will fail. * gnu/packages/bioinformatics.scm (htslib)[inputs]: Add bzip2 and xz. Signed-off-by: Efraim Flashner --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 693158798a..9c7ef41cc1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8,7 +8,7 @@ ;;; Copyright © 2016, 2020, 2022 Marius Bakke ;;; Copyright © 2016, 2018 Raoul Bonnal ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice -;;; Copyright © 2017, 2021 Arun Isaac +;;; Copyright © 2017, 2021, 2022 Arun Isaac ;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; Copyright © 2018 Gábor Boskovits ;;; Copyright © 2018, 2019, 2020, 2021 Mădălin Ionel Patrașcu @@ -4788,7 +4788,7 @@ performance.") "--enable-libcurl" "--enable-s3"))) (inputs - (list curl openssl)) + (list bzip2 curl openssl xz)) ;; This is referred to in the pkg-config file as a required library. (propagated-inputs (list zlib)) -- cgit v1.2.3 From 1ca9d9e1942b674cd2a4ce55ebfebc4485870366 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Thu, 31 Mar 2022 12:58:49 +0530 Subject: gnu: Add wfmash. * gnu/packages/bioinformatics.scm (wfmash): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/bioinformatics.scm | 45 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9c7ef41cc1..7a7f2f722e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -16124,3 +16124,48 @@ workflows from concise descriptions in ccwl. It is implemented as an @acronym{EDSL, Embedded Domain Specific Language} in the Scheme programming language.") (license license:gpl3+))) + +(define-public wfmash + (package + (name "wfmash") + (version "0.8.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/ekg/wfmash/releases/download/v" + version "/wfmash-v" version ".tar.gz")) + (sha256 + (base32 + "031cm1arpfckvihb28vlk69mirpnmlag81zcscfba1bac58wvr7c")) + (snippet + #~(begin + (use-modules (guix build utils)) + ;; Unbundle atomic-queue. + (delete-file-recursively "src/common/atomic_queue") + (substitute* "src/align/include/computeAlignments.hpp" + (("\"common/atomic_queue/atomic_queue.h\"") + "")) + ;; Remove compiler optimizations. + (substitute* (find-files "." "CMakeLists\\.txt") + (("-mcx16 ") "") + (("-march=native ") "")) + ;; Allow building on architectures other than x86_64. + (substitute* "src/common/dset64.hpp" + (("!__x86_64__") "0")))))) + (build-system cmake-build-system) + (arguments + (list #:tests? #f)) ; no tests + (inputs + (list atomic-queue + gsl + htslib + jemalloc + zlib)) + (synopsis "Base-accurate DNA sequence aligner") + (description "@code{wfmash} is a DNA sequence read mapper based on mash +distances and the wavefront alignment algorithm. It is a fork of MashMap that +implements base-level alignment via the wflign tiled wavefront global +alignment algorithm. It completes MashMap with a high-performance alignment +module capable of computing base-level alignments for very large sequences.") + (home-page "https://github.com/ekg/wfmash") + (license license:expat))) -- cgit v1.2.3 From 8f3dc994bbcb3028318e3d597f829a12396110c2 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 31 Mar 2022 16:13:57 +0300 Subject: gnu: wfmash: Enable test suite. * gnu/packages/bioinformatics.scm (wfmash)[arguments]: Don't disable tests. Add custom 'check phase based on upstream's own CI tests. [native-inputs]: Add samtools. --- gnu/packages/bioinformatics.scm | 109 +++++++++++++++++++++++++++++++++++++++- 1 file changed, 108 insertions(+), 1 deletion(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7a7f2f722e..fd659b59f8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -16154,13 +16154,120 @@ language.") (("!__x86_64__") "0")))))) (build-system cmake-build-system) (arguments - (list #:tests? #f)) ; no tests + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + ;; Adapted from .github/workflows/test_on_push.yml + (lambda* (#:key tests? inputs #:allow-other-keys) + (when tests? + (let ((samtools (search-input-file inputs "/bin/samtools"))) + ;; This is the easiest way to access the data + ;; needed for the test suite. + (symlink (string-append "../wfmash-v" #$version "/data") + "data") + (and + ;; This test takes 60 minutes on riscv64-linux. + #$@(if (not (target-riscv64?)) + #~((begin + ;; Test with a subset of the LPA dataset (PAF output) + (setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1") + (setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1") + (with-output-to-file "LPA.subset.paf" + (lambda _ + (invoke "bin/wfmash" + "data/LPA.subset.fa.gz" + "data/LPA.subset.fa.gz" + "-X" "-n" "10" "-T" "wflign_info." + "-u" "./"))) + (invoke "head" "LPA.subset.paf"))) + #~()) + ;; This test takes about 5 hours on riscv64-linux. + #$@(if (not (target-riscv64?)) + #~((begin + ;; Test with a subset of the LPA dataset (SAM output) + (setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1") + (setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1") + (with-output-to-file "LPA.subset.sam" + (lambda _ + (invoke "bin/wfmash" + "data/LPA.subset.fa.gz" + "data/LPA.subset.fa.gz" + "-X" "-N" "-a" "-T" "wflign_info."))) + (with-output-to-file "LPA.subset.sam-view" + (lambda _ + (invoke samtools "view" "LPA.subset.sam" "-bS"))) + (with-output-to-file "LPA.subset.bam" + (lambda _ + (invoke samtools "sort" "LPA.subset.sam-view"))) + (invoke samtools "index" "LPA.subset.bam") + ;; samtools view LPA.subset.bam | head | cut -f 1-9 + ;(invoke samtools "view" "LPA.subset.bam") + ;; There should be an easier way to do this with pipes. + (with-output-to-file "LPA.subset.bam-incr1" + (lambda _ + (invoke samtools "view" "LPA.subset.bam"))) + (with-output-to-file "LPA.subset.bam-incr2" + (lambda _ + (invoke "head" "LPA.subset.bam-incr1"))) + (invoke "cut" "-f" "1-9" "LPA.subset.bam-incr2"))) + #~()) + ;; This test takes 60 minutes on riscv64-linux. + #$@(if (not (target-riscv64?)) + #~((begin + ;; Test with a subset of the LPA dataset, + ;; setting a lower identity threshold (PAF output) + (setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1") + (setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1") + (with-output-to-file "LPA.subset.p90.paf" + (lambda _ + (invoke "bin/wfmash" + "data/LPA.subset.fa.gz" + "data/LPA.subset.fa.gz" + "-X" "-p" "90" "-n" "10" + "-T" "wflign_info."))) + (invoke "head" "LPA.subset.p90.paf"))) + #~()) + (begin + ;; Test aligning short reads (500 bps) to a reference (SAM output) + (setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1") + (setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1") + (with-output-to-file "reads.500bps.sam" + (lambda _ + (invoke "bin/wfmash" + "data/reference.fa.gz" + "data/reads.500bps.fa.gz" + "-s" "0.5k" "-N" "-a"))) + (with-output-to-file "reads.500bps.sam-view" + (lambda _ + (invoke samtools "view" "reads.500bps.sam" "-bS"))) + (with-output-to-file "reads.500bps.bam" + (lambda _ + (invoke samtools "sort" "reads.500bps.sam-view"))) + (invoke samtools "index" "reads.500bps.bam") + (with-output-to-file "reads.500bps.bam-view" + (lambda _ + (invoke samtools "view" "reads.500bps.bam"))) + (invoke "head" "reads.500bps.bam-view")) + (begin + ;; Test with few very short reads (255bps) (PAF output) + (setenv "ASAN_OPTIONS" "detect_leaks=1:symbolize=1") + (setenv "LSAN_OPTIONS" "verbosity=0:log_threads=1") + (with-output-to-file "reads.255bps.paf" + (lambda _ + (invoke "bin/wfmash" + "data/reads.255bps.fa.gz" + "data/reads.255bps.fa.gz" + "-X" "-w" "16"))) + (invoke "head" "reads.255bps.paf")))))))))) (inputs (list atomic-queue gsl htslib jemalloc zlib)) + (native-inputs + (list samtools)) (synopsis "Base-accurate DNA sequence aligner") (description "@code{wfmash} is a DNA sequence read mapper based on mash distances and the wavefront alignment algorithm. It is a fork of MashMap that -- cgit v1.2.3 From 05e68f31ba88586ba6b958b1a76f613f64c0c9cc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 31 Mar 2022 16:01:27 +0200 Subject: gnu: python-velocyto: Set cache directory for Numba. * gnu/packages/bioinformatics.scm (python-velocyto)[arguments]: Add phase 'set-numba-cache-dir. --- gnu/packages/bioinformatics.scm | 7 +++++++ 1 file changed, 7 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fd659b59f8..fd7d70c6b4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13519,6 +13519,13 @@ repeated areas between contigs.") (snippet '(for-each delete-file (find-files "." "\\.c"))))) (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + ;; Numba needs a writable dir to cache functions. + (add-before 'check 'set-numba-cache-dir + (lambda _ + (setenv "NUMBA_CACHE_DIR" "/tmp")))))) (native-inputs (list python-joblib)) (propagated-inputs -- cgit v1.2.3 From 855c8d9d41ef2f5d8c9a2fc952a27eda32105585 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 4 Apr 2022 22:41:54 +0300 Subject: gnu: smithwaterman: Fix cross-compiling. * gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Add make-flag to use cxx-for-target. Adjust custom 'patch-source and 'build-dynamic phases to use cross toolchain binaries when cross compiling. Remove trailing #t from phases. --- gnu/packages/bioinformatics.scm | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fd7d70c6b4..b52fa1a61a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14182,7 +14182,8 @@ some of the details of opening and jumping in tabix-indexed files.") (build-system gnu-build-system) (arguments `(#:tests? #f ; There are no tests to run. - #:make-flags '("libsw.a" "all") + #:make-flags (list (string-append "CXX=" ,(cxx-for-target)) + "libsw.a" "all") #:phases (modify-phases %standard-phases (delete 'configure) ; There is no configure phase. @@ -14190,10 +14191,14 @@ some of the details of opening and jumping in tabix-indexed files.") (lambda _ (substitute* "Makefile" (("-c ") "-c -fPIC ")) - #t)) + ,@(if (%current-target-system) + `((substitute* "Makefile" + (("ld") (string-append ,(%current-target-system) "-ld")) + (("ar") (string-append ,(%current-target-system) "-ar")))) + '()))) (add-after 'build 'build-dynamic (lambda _ - (invoke "g++" + (invoke ,(cxx-for-target) "-shared" "-o" "libsmithwaterman.so" "smithwaterman.o" "SmithWatermanGotoh.o" "disorder.o" "BandedSmithWaterman.o" @@ -14224,8 +14229,7 @@ some of the details of opening and jumping in tabix-indexed files.") Description: smith-waterman-gotoh alignment algorithm~@ Libs: -L${libdir} -lsmithwaterman~@ Cflags: -I${includedir}~%" - out ,version)))) - #t))))) + out ,version))))))))) (home-page "https://github.com/ekg/smithwaterman") (synopsis "Implementation of the Smith-Waterman algorithm") (description "Implementation of the Smith-Waterman algorithm.") -- cgit v1.2.3 From c1fc65ecb63b725ab770f20a3221be83f64dc68c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 4 Apr 2022 22:45:37 +0300 Subject: gnu: smithwaterman: Use new style for phases. * gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Use list of G-Expressions. --- gnu/packages/bioinformatics.scm | 98 +++++++++++++++++++++-------------------- 1 file changed, 50 insertions(+), 48 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b52fa1a61a..82d9a3eca6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14181,55 +14181,57 @@ some of the details of opening and jumping in tabix-indexed files.") (base32 "0i9d8zrxpiracw3mxzd9siybpy62p06rqz9mc2w93arajgbk45bs")))) (build-system gnu-build-system) (arguments - `(#:tests? #f ; There are no tests to run. - #:make-flags (list (string-append "CXX=" ,(cxx-for-target)) - "libsw.a" "all") + (list + #:tests? #f ; There are no tests to run. + #:make-flags + #~(list (string-append "CXX=" #$(cxx-for-target)) + "libsw.a" "all") #:phases - (modify-phases %standard-phases - (delete 'configure) ; There is no configure phase. - (add-after 'unpack 'patch-source - (lambda _ - (substitute* "Makefile" - (("-c ") "-c -fPIC ")) - ,@(if (%current-target-system) - `((substitute* "Makefile" - (("ld") (string-append ,(%current-target-system) "-ld")) - (("ar") (string-append ,(%current-target-system) "-ar")))) - '()))) - (add-after 'build 'build-dynamic - (lambda _ - (invoke ,(cxx-for-target) - "-shared" "-o" "libsmithwaterman.so" - "smithwaterman.o" "SmithWatermanGotoh.o" - "disorder.o" "BandedSmithWaterman.o" - "LeftAlign.o" "Repeats.o" "IndelAllele.o"))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin")) - (lib (string-append out "/lib"))) - (install-file "smithwaterman" bin) - (for-each - (lambda (file) - (install-file file (string-append out "/include/smithwaterman"))) - (find-files "." "\\.h$")) - (install-file "libsmithwaterman.so" lib) - (install-file "libsw.a" lib) - (mkdir-p (string-append lib "/pkgconfig")) - (with-output-to-file (string-append lib "/pkgconfig/smithwaterman.pc") - (lambda _ - (format #t "prefix=~a~@ - exec_prefix=${prefix}~@ - libdir=${exec_prefix}/lib~@ - includedir=${prefix}/include/smithwaterman~@ - ~@ - ~@ - Name: smithwaterman~@ - Version: ~a~@ - Description: smith-waterman-gotoh alignment algorithm~@ - Libs: -L${libdir} -lsmithwaterman~@ - Cflags: -I${includedir}~%" - out ,version))))))))) + #~(modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (add-after 'unpack 'patch-source + (lambda _ + (substitute* "Makefile" + (("-c ") "-c -fPIC ")) + #$@(if (%current-target-system) + #~((substitute* "Makefile" + (("ld") (string-append #$(%current-target-system) "-ld")) + (("ar") (string-append #$(%current-target-system) "-ar")))) + '()))) + (add-after 'build 'build-dynamic + (lambda _ + (invoke #$(cxx-for-target) + "-shared" "-o" "libsmithwaterman.so" + "smithwaterman.o" "SmithWatermanGotoh.o" + "disorder.o" "BandedSmithWaterman.o" + "LeftAlign.o" "Repeats.o" "IndelAllele.o"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (lib (string-append out "/lib"))) + (install-file "smithwaterman" bin) + (for-each + (lambda (file) + (install-file file (string-append out "/include/smithwaterman"))) + (find-files "." "\\.h$")) + (install-file "libsmithwaterman.so" lib) + (install-file "libsw.a" lib) + (mkdir-p (string-append lib "/pkgconfig")) + (with-output-to-file (string-append lib "/pkgconfig/smithwaterman.pc") + (lambda _ + (format #t "prefix=~a~@ + exec_prefix=${prefix}~@ + libdir=${exec_prefix}/lib~@ + includedir=${prefix}/include/smithwaterman~@ + ~@ + ~@ + Name: smithwaterman~@ + Version: ~a~@ + Description: smith-waterman-gotoh alignment algorithm~@ + Libs: -L${libdir} -lsmithwaterman~@ + Cflags: -I${includedir}~%" + out #$version))))))))) (home-page "https://github.com/ekg/smithwaterman") (synopsis "Implementation of the Smith-Waterman algorithm") (description "Implementation of the Smith-Waterman algorithm.") -- cgit v1.2.3 From 345f79b2cf02ecd187a1e3c922f685f3fc58bf2e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 4 Apr 2022 22:58:25 +0300 Subject: gnu: freebayes: Fix test suite. * gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Add python. --- gnu/packages/bioinformatics.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 82d9a3eca6..eed7e54f7f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14512,6 +14512,7 @@ manipulations on VCF files.") ("parallel" ,parallel) ("perl" ,perl) ("pkg-config" ,pkg-config) + ("python" ,python) ("samtools" ,samtools) ("simde" ,simde) ;; This submodule is needed to run the tests. -- cgit v1.2.3 From 5d1c9fcdcf81bb95516f2d44e293c760300c9589 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 5 Apr 2022 17:26:00 +0200 Subject: gnu: pigx-scrnaseq: Update to 1.1.8. * gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.8. [patches]: Remove. [native-inputs]: Remove. * gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/bioinformatics.scm | 12 ++------ .../patches/pigx-scrnaseq-no-citeproc.patch | 33 ---------------------- 3 files changed, 3 insertions(+), 43 deletions(-) delete mode 100644 gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/local.mk b/gnu/local.mk index f5e2702031..420aa91d86 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1627,7 +1627,6 @@ dist_patch_DATA = \ %D%/packages/patches/pidgin-add-search-path.patch \ %D%/packages/patches/pigx-bsseq-no-citeproc.patch \ %D%/packages/patches/pigx-chipseq-no-citeproc.patch \ - %D%/packages/patches/pigx-scrnaseq-no-citeproc.patch \ %D%/packages/patches/pinball-system-ltdl.patch \ %D%/packages/patches/pingus-boost-headers.patch \ %D%/packages/patches/pingus-sdl-libs-config.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index eed7e54f7f..3ad8800fdb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11132,7 +11132,7 @@ methylation and segmentation.") (define-public pigx-scrnaseq (package (name "pigx-scrnaseq") - (version "1.1.7") + (version "1.1.8") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/" @@ -11140,20 +11140,14 @@ methylation and segmentation.") "/pigx_scrnaseq-" version ".tar.gz")) (sha256 (base32 - "1h5mcxzwj3cidlkvy9ly5wmi48vwfsjf8dxjfirknqxr9a92hwlx")) - (patches (search-patches "pigx-scrnaseq-no-citeproc.patch")))) + "1lc42hl8mz95kilh0z39s3wnv092mhm6vl2i394n0yfvdzk4f885")))) (build-system gnu-build-system) (arguments - `(#:phases + '(#:phases (modify-phases %standard-phases - (add-before 'bootstrap 'autoreconf - (lambda _ - (invoke "autoreconf" "-vif"))) (add-before 'configure 'set-PYTHONPATH (lambda _ (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))))) - (native-inputs - (list automake autoconf)) (inputs `(("coreutils" ,coreutils) ("perl" ,perl) diff --git a/gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch b/gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch deleted file mode 100644 index 4cce33fb01..0000000000 --- a/gnu/packages/patches/pigx-scrnaseq-no-citeproc.patch +++ /dev/null @@ -1,33 +0,0 @@ -diff -Naur pigx_scrnaseq-1.1.7/configure.ac pigx_scrnaseq-1.1.7.patched/configure.ac ---- pigx_scrnaseq-1.1.7/configure.ac 2020-03-17 14:37:46.000000000 +0100 -+++ pigx_scrnaseq-1.1.7.patched/configure.ac 2021-10-06 13:55:49.779271317 +0200 -@@ -43,7 +43,6 @@ - find_or_override_prog([GNUBASH], [bash]) - find_or_override_prog([SNAKEMAKE], [snakemake]) - find_or_override_prog([PANDOC], [pandoc]) --find_or_override_prog([PANDOC_CITEPROC], [pandoc-citeproc]) - find_or_override_prog([FASTQC], [fastqc]) - find_or_override_prog([STAR], [STAR]) - find_or_override_prog([SAMTOOLS], [samtools]) -diff -Naur pigx_scrnaseq-1.1.7/Makefile.in pigx_scrnaseq-1.1.7.patched/Makefile.in ---- pigx_scrnaseq-1.1.7/Makefile.in 2020-11-30 16:55:48.000000000 +0100 -+++ pigx_scrnaseq-1.1.7.patched/Makefile.in 2021-10-06 13:55:52.224340194 +0200 -@@ -395,7 +395,6 @@ - PACKAGE_URL = @PACKAGE_URL@ - PACKAGE_VERSION = @PACKAGE_VERSION@ - PANDOC = @PANDOC@ --PANDOC_CITEPROC = @PANDOC_CITEPROC@ - PATH_SEPARATOR = @PATH_SEPARATOR@ - PERL = @PERL@ - PYTHON = @PYTHON@ -diff -Naur pigx_scrnaseq-1.1.7/pigx-scrnaseq.in pigx_scrnaseq-1.1.7.patched/pigx-scrnaseq.in ---- pigx_scrnaseq-1.1.7/pigx-scrnaseq.in 2020-11-30 16:08:55.000000000 +0100 -+++ pigx_scrnaseq-1.1.7.patched/pigx-scrnaseq.in 2021-10-06 13:55:47.889218079 +0200 -@@ -274,7 +274,6 @@ - if path.exists(bin): shutil.rmtree(bin) - os.makedirs(bin, exist_ok=True) - os.symlink('@PANDOC@', path.join(bin, "pandoc")) -- os.symlink('@PANDOC_CITEPROC@', path.join(bin, "pandoc-citeproc")) - os.symlink('@RSCRIPT@', path.join(bin, "Rscript")) - os.environ['PATH'] = path.abspath(bin) + ":" + os.environ['PATH'] - os.environ['PIGX_PATH'] = path.abspath(bin) + ":" + os.environ['PATH'] -- cgit v1.2.3 From e721122069528b38e9dc901c4ca69acba0df5aea Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 5 Apr 2022 17:26:53 +0200 Subject: gnu: pigx-scrnaseq: Use new inputs style. * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Use plain list. --- gnu/packages/bioinformatics.scm | 85 +++++++++++++++++++++-------------------- 1 file changed, 43 insertions(+), 42 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3ad8800fdb..5ca1104436 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11149,50 +11149,51 @@ methylation and segmentation.") (lambda _ (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))))) (inputs - `(("coreutils" ,coreutils) - ("perl" ,perl) - ("fastqc" ,fastqc) - ("flexbar" ,flexbar) - ("java" ,icedtea-8) - ("jellyfish" ,jellyfish) - ("python-wrapper" ,python-wrapper) - ("python-pyyaml" ,python-pyyaml) - ("python-pandas" ,python-pandas) - ("python-magic" ,python-magic) - ("python-numpy" ,python-numpy) - ("python-loompy" ,python-loompy) - ("pandoc" ,pandoc) - ("samtools" ,samtools) - ("snakemake" ,snakemake) - ("star" ,star-for-pigx) - ("r-minimal" ,r-minimal) - ("r-argparser" ,r-argparser) - ("r-cowplot" ,r-cowplot) - ("r-data-table" ,r-data-table) - ("r-delayedarray" ,r-delayedarray) - ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dplyr" ,r-dplyr) - ("r-dropbead" ,r-dropbead) - ("r-dt" ,r-dt) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicfiles" ,r-genomicfiles) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-hdf5array" ,r-hdf5array) - ("r-pheatmap" ,r-pheatmap) - ("r-rmarkdown" ,r-rmarkdown) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-rtsne" ,r-rtsne) - ("r-scater" ,r-scater) - ("r-scran" ,r-scran) - ("r-seurat" ,r-seurat) - ("r-singlecellexperiment" ,r-singlecellexperiment) - ("r-stringr" ,r-stringr) - ("r-yaml" ,r-yaml))) + (list coreutils + perl + fastqc + flexbar + icedtea-8 + jellyfish + python-wrapper + python-pyyaml + python-pandas + python-magic + python-numpy + python-loompy + pandoc + samtools + snakemake + star-for-pigx + r-minimal + r-argparser + r-cowplot + r-data-table + r-delayedarray + r-delayedmatrixstats + r-dplyr + r-dropbead + r-dt + r-genomicalignments + r-genomicfiles + r-genomicranges + r-ggplot2 + r-hdf5array + r-pheatmap + r-rmarkdown + r-rsamtools + r-rtracklayer + r-rtsne + r-scater + r-scran + r-seurat + r-singlecellexperiment + r-stringr + r-yaml)) (home-page "https://bioinformatics.mdc-berlin.de/pigx/") (synopsis "Analysis pipeline for single-cell RNA sequencing experiments") - (description "PiGX scRNAseq is an analysis pipeline for preprocessing and + (description + "PiGX scRNAseq is an analysis pipeline for preprocessing and quality control for single cell RNA sequencing experiments. The inputs are read files from the sequencing experiment, and a configuration file which describes the experiment. It produces processed files for downstream analysis -- cgit v1.2.3 From df2dc0c41644477c8cc3ccc958b822f8440114ef Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 5 Apr 2022 18:35:14 +0200 Subject: gnu: pigx-scrnaseq: Set NUMBA_CACHE_DIR. This is needed since the update of python-loompy. * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[arguments]: Rename 'set-PYTHONPATH to 'set-additional-environment-variables and set NUMBA_CACHE_DIR. --- gnu/packages/bioinformatics.scm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5ca1104436..e9778831d2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11145,8 +11145,11 @@ methylation and segmentation.") (arguments '(#:phases (modify-phases %standard-phases - (add-before 'configure 'set-PYTHONPATH + (add-before 'configure 'set-additional-environment-variables (lambda _ + ;; Needed because of loompy + (setenv "NUMBA_CACHE_DIR" "/tmp") + ;; Needed to capture environment (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH"))))))) (inputs (list coreutils -- cgit v1.2.3 From e3e3381fdbc56f351063d9b4a49e99645b20d7d3 Mon Sep 17 00:00:00 2001 From: Hong Li Date: Tue, 29 Mar 2022 07:04:02 +0000 Subject: gnu: Add r-rnaseqdtu. * gnu/packages/bioinformatics.scm (r-rnaseqdtu): New variable. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e9778831d2..106b25a50b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9009,6 +9009,43 @@ for analyzing gene-level association tests in meta-analyses for binary trait.") (license license:gpl3))) +(define-public r-rnaseqdtu + (let ((commit "5bee1e769d2e1dc6a3f1cecb78078050eeb5b9ac") + (revision "1")) + (package + (name "r-rnaseqdtu") + (version (git-version "2.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mikelove/rnaseqDTU/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0jfi1ydsk8m5nadwnih48v87nnxdc7s3f0pny4axmnj40dd42as0")))) + (properties `((upstream-name . "rnaseqDTU"))) + (build-system r-build-system) + (propagated-inputs + (list r-deseq2 + r-devtools + r-dexseq + r-drimseq + r-edger + r-rafalib + r-stager)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/mikelove/rnaseqDTU/") + (synopsis "RNA-seq workflow for differential transcript usage") + (description + "This package provides an RNA-seq workflow for differential transcript +usage (DTU) following Salmon quantification. This workflow performs a DTU +analysis on simulated data. It also shows how to use stageR to perform +two-stage testing of DTU, a statistical framework to screen at the gene level +and then confirm which transcripts within the significant genes show evidence +of DTU.") + (license license:artistic2.0)))) + (define-public r-dropbead (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247") (revision "2")) -- cgit v1.2.3 From 96a132809f0196d6a08f6c5c6900846d9859beb2 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sun, 10 Apr 2022 20:46:01 +0300 Subject: gnu: smithwaterman: Fix cross-compiling. The 'ar' matched the 'ar' in 'aarch64-linux-gnu' to unfun consequences. * gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: More closely match the 'ar' and 'ld' commands when substituting them. --- gnu/packages/bioinformatics.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 106b25a50b..0755b035e6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14230,8 +14230,10 @@ some of the details of opening and jumping in tabix-indexed files.") (("-c ") "-c -fPIC ")) #$@(if (%current-target-system) #~((substitute* "Makefile" - (("ld") (string-append #$(%current-target-system) "-ld")) - (("ar") (string-append #$(%current-target-system) "-ar")))) + (("\tld") + (string-append "\t" #$(%current-target-system) "-ld")) + (("\tar") + (string-append "\t" #$(%current-target-system) "-ar")))) '()))) (add-after 'build 'build-dynamic (lambda _ -- cgit v1.2.3 From 6413d0898b92efda8213b3ced0b6d1c736726b89 Mon Sep 17 00:00:00 2001 From: zimoun Date: Fri, 8 Apr 2022 16:59:54 +0200 Subject: gnu: Add r-copykat. * gnu/packages/bioinformatics.scm (r-copykat): New variable. --- gnu/packages/bioinformatics.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0755b035e6..e3bbdaa380 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9138,6 +9138,44 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") communication networks from scRNA-seq data.") (license license:gpl3)))) +(define-public r-copykat + (let ((commit ;no tag + "256de33dfc1b80a1a0ac9e098c5557f95a4e0d53") + (revision "0")) + (package + (name "r-copykat") + (version (git-version "1.0.8" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/navinlabcode/copykat") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ckyqnial3imcqlgd6xfgwk5w977l1i87sx4kdbwdvg40w0vh1j8")))) + (properties `((upstream-name . "copykat"))) + (build-system r-build-system) + (propagated-inputs + (list r-cluster + r-dlm + r-gplots + r-mcmcpack + r-mixtools + r-paralleldist + r-rcolorbrewer)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/navinlabcode/copykat") + (synopsis "Inference of genomic copy number from single cell RNAseq data") + (description + "This package Copynumber KAryotyping of Tumors infers genomic copy +number and subclonal structure of human tumors using integrative Bayesian +approaches to identify genome-wide aneuploidy at 5MB resolution in single +cells data. It separates tumor cells and tumor subclones from normal cells +using high-throughput sc-RNAseq data.") + (license license:gpl2)))) + (define-public sambamba (package (name "sambamba") -- cgit v1.2.3 From c8a6e4abbc4f279f919017d238576cf8724e9456 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 14 Apr 2022 13:35:22 +0200 Subject: gnu: r-chromvarmotifs: Move to (gnu packages bioinformatics). * gnu/packages/bioconductor.scm (r-chromvarmotifs): Move this variable from here... * gnu/packages/bioinformatics.scm (r-chromvarmotifs): ...to here. --- gnu/packages/bioconductor.scm | 28 ---------------------------- gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++ 2 files changed, 28 insertions(+), 28 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ecb188a84f..f795b6ad9c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1211,34 +1211,6 @@ single-cell data or deconvolution of bulk RNA-seq.") chromstaR package.") (license license:gpl3))) -(define-public r-chromvarmotifs - (let ((commit "38bed559c1f4770b6c91c80bf3f8ea965da26076") - (revision "1")) - (package - (name "r-chromvarmotifs") - (version (git-version "0.2.0" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/GreenleafLab/chromVARmotifs") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0i9v1m1hrg1lkd2pnkj5nnrpks6vhhhpbdhsfl2lmjak4npxxr5q")))) - (properties `((upstream-name . "chromVARmotifs"))) - (build-system r-build-system) - (propagated-inputs - `(("r-tfbstools" ,r-tfbstools))) - (home-page "https://github.com/GreenleafLab/chromVARmotifs") - (synopsis "Stores motif collections for use with motifmatchr or chromVAR") - (description - "This package stores motif collections as lists of @dfn{position -frequency matrix} (PWMatrixList) objects provided by the @code{TFBSTools} -package for use in R with packages like @code{motifmatchr} or -@code{chromVAR}.") - (license license:expat)))) - (define-public r-copyhelper (package (name "r-copyhelper") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e3bbdaa380..b838c2dbfa 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8981,6 +8981,34 @@ analysis, variant tools is project based and provides a whole set of tools to manipulate and analyze genetic variants.") (license license:gpl3+))) +(define-public r-chromvarmotifs + (let ((commit "38bed559c1f4770b6c91c80bf3f8ea965da26076") + (revision "1")) + (package + (name "r-chromvarmotifs") + (version (git-version "0.2.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/GreenleafLab/chromVARmotifs") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0i9v1m1hrg1lkd2pnkj5nnrpks6vhhhpbdhsfl2lmjak4npxxr5q")))) + (properties `((upstream-name . "chromVARmotifs"))) + (build-system r-build-system) + (propagated-inputs + `(("r-tfbstools" ,r-tfbstools))) + (home-page "https://github.com/GreenleafLab/chromVARmotifs") + (synopsis "Stores motif collections for use with motifmatchr or chromVAR") + (description + "This package stores motif collections as lists of @dfn{position +frequency matrix} (PWMatrixList) objects provided by the @code{TFBSTools} +package for use in R with packages like @code{motifmatchr} or +@code{chromVAR}.") + (license license:expat)))) + (define-public r-raremetals2 (package (name "r-raremetals2") -- cgit v1.2.3 From 7034746e15c1ef1fac507f59e270b99e3e6c482c Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 14 Apr 2022 22:55:33 +0300 Subject: gnu: scregseg: Remove cythonized file. * gnu/packages/bioinformatics.scm (scregseg)[source]: Add snippet to remove cythonized file. --- gnu/packages/bioinformatics.scm | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b838c2dbfa..8f2f69530f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15894,7 +15894,11 @@ populations.") (file-name (git-file-name name version)) (sha256 (base32 - "1k8hllr5if6k2mm2zj391fv40sfc008cjm04l9vgfsdppb80i112")))) + "1k8hllr5if6k2mm2zj391fv40sfc008cjm04l9vgfsdppb80i112")) + (snippet + #~(begin + (use-modules ((guix build utils))) + (delete-file "src/scregseg/_utils.c"))))) (build-system python-build-system) (arguments `(#:tests? #false ; tests require network access -- cgit v1.2.3 From ffb616b69dced25b840f2e5178062072d89623eb Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 19 Apr 2022 21:54:57 +0300 Subject: gnu: vcflib: Update to 1.0.3. * gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.3. [source]: Remove trailing #t. [arguments]: Remove trailing #t from phases. --- gnu/packages/bioinformatics.scm | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8f2f69530f..4634b86515 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14478,7 +14478,7 @@ library automatically handles index file generation and use.") (define-public vcflib (package (name "vcflib") - (version "1.0.2") + (version "1.0.3") (source (origin (method git-fetch) @@ -14487,7 +14487,7 @@ library automatically handles index file generation and use.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1k1z3876kbzifj1sqfzsf3lgb4rw779hvkg6ryxbyq5bc2paj9kh")) + (base32 "1r7pnajg997zdjkf1b38m14v0zqnfx52w7nbldwh1xpbpahb1hjh")) (modules '((guix build utils))) (snippet '(begin @@ -14510,8 +14510,7 @@ library automatically handles index file generation and use.") (("Fasta.h") "fastahack/Fasta.h")) (for-each delete-file-recursively '("fastahack" "filevercmp" "fsom" "googletest" "intervaltree" - "libVCFH" "multichoose" "smithwaterman")) - #t)))) + "libVCFH" "multichoose" "smithwaterman")))))) (build-system cmake-build-system) (inputs (list bzip2 @@ -14540,8 +14539,7 @@ library automatically handles index file generation and use.") (substitute* "CMakeLists.txt" (("vcflib STATIC") "vcflib SHARED")) (substitute* "test/Makefile" - (("libvcflib.a") "libvcflib.so")) - #t)) + (("libvcflib.a") "libvcflib.so")))) (add-after 'unpack 'unpack-submodule-sources (lambda* (#:key inputs #:allow-other-keys) (let ((unpack (lambda (source target) @@ -14556,8 +14554,7 @@ library automatically handles index file generation and use.") (unpack "filevercmp-src" "filevercmp") (unpack "fsom-src" "fsom") (unpack "intervaltree-src" "intervaltree") - (unpack "multichoose-src" "multichoose")) - #t))) + (unpack "multichoose-src" "multichoose"))))) ;; This pkg-config file is provided by other distributions. (add-after 'install 'install-pkg-config-file (lambda* (#:key outputs #:allow-other-keys) -- cgit v1.2.3 From 33fe027f91062926c513c3b5f9a91ae761810f89 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 26 Apr 2022 09:47:51 +0200 Subject: gnu: Add r-giotto. * gnu/packages/bioinformatics.scm (r-giotto): New variable. --- gnu/packages/bioinformatics.scm | 58 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 58 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4634b86515..40ccba247c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11972,6 +11972,64 @@ cells with similar identification cards in the different cytometric profiles is then merged.") (license license:gpl2)))) +(define-public r-giotto + (let ((commit "68d7390dce87223cac11d4d8f31705fe0144d011") + (revision "1")) + (package + (name "r-giotto") + (version (git-version "1.1.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/RubD/Giotto/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0mv60khc05wrxzr4ir6cirn7dpqvgwan5hm00lmafsyalr51nf5i")))) + (properties `((upstream-name . "Giotto"))) + (build-system r-build-system) + (propagated-inputs + (list r-clusterr + r-complexheatmap + r-cowplot + r-data-table + r-dbscan + r-deldir + r-farver + r-fitdistrplus + r-ggdendro + r-ggplot2 + r-ggraph + r-ggrepel + r-igraph + r-irlba + r-lfa + r-limma + r-magick + r-magrittr + r-matrix + r-matrixstats + r-plotly + r-qvalue + r-r-utils + r-rcolorbrewer + r-rcpp + r-reshape2 + r-reticulate + r-rfast + r-rlang + r-rtsne + r-scales + r-uwot)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/RubD/Giotto/") + (synopsis "Spatial single-cell transcriptomics toolbox") + (description + "This package provides a toolbox to process, analyze and visualize +spatial single-cell expression data.") + (license license:expat)))) + (define-public gffread ;; We cannot use the tagged release because it is not in sync with gclib. ;; See https://github.com/gpertea/gffread/issues/26 -- cgit v1.2.3