| Commit message (Collapse) | Author | Age |
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* gnu/packages/bioinformatics.scm (delly): New variable.
* gnu/packages/patches/delly-use-system-libraries.patch: New file.
* gnu/local.mk: Include delly-use-system-libraries.patch.
Signed-off-by: Leo Famulari <leo@famulari.name>
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* gnu/packages/bioinformatics.scm (mash): Update to 2.0.
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* gnu/packages/bioinformatics.scm (mafft): Update to 7.394.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.19.
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* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.3;
[propagated-inputs]: Remove r-gridextra.
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* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.2;
[inputs]: Add zlib.
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* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.2.
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This package propagates r-rmarkdown, which propagates its own variant of
Pandoc.
* gnu/packages/bioinformatics.scm (r-bookdown)[propagated-inputs]: Remove
ghc-pandoc.
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* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.10.
[inputs]: Remove r-rcas and duplicate of snakemake; add r-biocparallel,
r-biostrings, r-dplyr, r-genomicalignments, rsamtools, r-s4vectors, r-tibble,
r-tidyr, r-htmlwidgets, and r-rmarkdown.
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* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.9.
[inputs]: Add coreutils and grep.
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* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.8.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.3.
[inputs]: Add gzip.
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* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.7.
[inputs]: Add coreutils, sed, and grep.
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* gnu/packages/bioinformatics.scm (bismark)[arguments]: Keep reference to
gunzip executable.
[inputs]: Add gzip.
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* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.3.
[inputs]: Add coreutils and perl.
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* gnu/packages/bioinformatics.scm (pigx): Update to 0.0.2.
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* gnu/packages/bioinformatics.scm (r-rcas)[inputs]: Replace
ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1.
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* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.8.
[inputs]: Add python-magic, python-xlrd, and trim-galore.
[arguments]: Disable tests.
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* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
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* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
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* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
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* gnu/packages/bioinformatics.scm (pigx): New variable.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase to
disable a memory hungry test.
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* gnu/packages/bioinformatics.scm (pigx-scrnaseq): New variable.
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* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Replace mysql with
mariadb.
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* gnu/packages/bioinformatics.scm (r-diversitree): New variable.
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* gnu/packages/bioinformatics.scm (pigx-bsseq): New variable.
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* gnu/packages/bioinformatics.scm (pigx-chipseq): New variable.
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* gnu/packages/bioinformatics.scm (r-rhdf5lib)[arguments]: Remove timestamp
and host system kernel version.
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* gnu/packages/bioinformatics.scm (r-phangorn): New variable.
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* gnu/packages/bioinformatics.scm (r-ape): Move from here...
* gnu/packages/cran.scm (r-ape): ...to here.
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* gnu/packages/bioinformatics.scm (r-dropbead): Update to 0-2.d746c6f.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq): New variable.
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* gnu/packages/bioinformatics.scm (samtools): Update to 1.7.
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* gnu/packages/bioinformatics.scm (htslib): Update to 1.7.
[arguments]: Remove field.
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* gnu/packages/bioinformatics.scm (r-rhdf5)[arguments]: Remove timestamp and
host system information from settings file.
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* gnu/packages/bioinformatics.scm (piranha)[source]: Declare a source
file-name.
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* gnu/packages/bioinformatics.scm (libdivsufsort)[source]: Declare a
source file-name.
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* gnu/packages/bioinformatics.scm (seek)[source]: Declare a source
file-name.
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* gnu/packages/bioinformatics.scm (r-dropbead)[source]: Declare a source
file-name.
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* gnu/packages/bioinformatics.scm (dropseq-tools): New variable.
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* gnu/packages/bioinformatics.scm (java-picard-2.10.3): New variable.
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* gnu/packages/bioinformatics.scm (java-htsjdk-2.10.1): New variable.
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* gnu/packages/bioinformatics.scm (java-htsjdk-latest): New variable.
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* gnu/packages/bioinformatics.scm (java-biojava-alignment-4.0): New variable.
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* gnu/packages/bioinformatics.scm (java-biojava-phylo-4.0): New variable.
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* gnu/packages/bioinformatics.scm (java-biojava-core-4.0): New variable.
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* gnu/packages/bioinformatics.scm (java-biojava-alignment): New variable.
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* gnu/packages/bioinformatics.scm (java-biojava-phylo): New variable.
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