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author | Kei Kebreau <kkebreau@posteo.net> | 2017-07-30 21:02:35 -0400 |
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committer | Kei Kebreau <kkebreau@posteo.net> | 2017-09-04 00:10:59 -0400 |
commit | d10092b849153dc27cfed0a9601fde6c7bdec918 (patch) | |
tree | 9c098d3591b62948335449d6f18f755f8a0f0f9e /gnu/packages/bioinformatics.scm | |
parent | 100b216d8a4218daec4a79024d62d54b52dc07be (diff) | |
download | guix-patches-d10092b849153dc27cfed0a9601fde6c7bdec918.tar guix-patches-d10092b849153dc27cfed0a9601fde6c7bdec918.tar.gz |
gnu: Put autoconf-related phases immediately after the 'unpack phase.
* gnu/packages/audio.scm (audacity, rtmidi)[arguments]: Correct phases
accordingly.
* gnu/packages/bioinformatics.scm (mash, seek, vsearch, emboss,
htslib-for-sambamba)[arguments]: Likewise.
* gnu/packages/ci.scm (cuirass)[arguments]: Likewise.
* gnu/packages/compression.scm (minizip, xdelta)[arguments]: Likewise.
* gnu/packages/cpp.scm (libzen)[arguments]: Likewise.
* gnu/packages/crypto.scm (opendht)[arguments]: Likewise.
* gnu/packages/databases.scm (4store, mdbtools)[arguments]: Likewise.
* gnu/packages/debug.scm (stress-make)[arguments]: Likewise.
* gnu/packages/dns.scm (dnscrypt-proxy, dnscrypt-wrapper)[arguments]:
Likewise.
* gnu/packages/emacs.scm (emacs-pdf-tools)[arguments]: Likewise.
* gnu/packages/embedded.scm (libjaylink, openocd)[arguments]: Likewise.
* gnu/packages/engineering.scm (gerbv)[arguments]: Likewise.
* gnu/packages/erlang.scm (erlang)[arguments]: Likewise.
* gnu/packages/ftp.scm (weex)[arguments]: Likewise.
* gnu/packages/gnome.scm (dia)[arguments]: Likewise.
* gnu/packages/gnunet.scm (gnurl, guile-gnunet)[arguments]: Likewise.
* gnu/packages/gtk.scm (guile-rsvg, graphene)[arguments]: Likewise.
* gnu/packages/guile.scm (guildhall, guile-ics, guile-sqlite3)[arguments]:
Likewise.
* gnu/packages/ibus.scm (ibus-libpinyin)[arguments]: Likewise.
* gnu/packages/irc.scm (weechat)[arguments]: Likewise.
* gnu/packages/java.scm (classpath-devel)[arguments]: Likewise.
* gnu/packages/libreoffice.scm (libetonyek)[arguments]: Likewise.
* gnu/packages/libusb.scm (hidapi)[arguments]: Likewise.
* gnu/packages/linux.scm (gpm)[arguments]: Likewise.
* gnu/packages/logging.scm (glog)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (ghmm)[arguments]: Likewise.
* gnu/packages/mail.scm (dovecot-trees, dovecot-libsodium-plugin, esmtp)
[arguments]: Likewise.
* gnu/packages/messaging.scm (freetalk, libmesode, libstrophe)[arguments]:
Likewise.
* gnu/packages/microcom.scm (microcom)[arguments]: Likewise.
* gnu/packages/ocaml.scm (ocaml-ssl)[arguments]: Likewise.
* gnu/packages/parallel.scm (slurm)[arguments]: Likewise.
* gnu/packages/pdf.scm (libharu)[arguments]: Likewise.
* gnu/packages/samba.scm (cifs-utils)[arguments]: Likewise.
* gnu/packages/serialization.scm (msgpack)[arguments]: Likewise.
* gnu/packages/shells.scm (scsh)[arguments]: Likewise.
* gnu/packages/telephony.scm (libiax2)[arguments]: Likewise.
* gnu/packages/textutils.scm (dotconf)[arguments]: Likewise.
* gnu/packages/version-control.scm (findnewest)[arguments]: Likewise.
* gnu/packages/video.scm (libmediainfo, mediainfo)[arguments]: Likewise.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r-- | gnu/packages/bioinformatics.scm | 14 |
1 files changed, 7 insertions, 7 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1f1b686c71..5e8eef4e1c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3450,7 +3450,7 @@ sequences).") (("^#include \"kseq\\.h\"") "#include \"htslib/kseq.h\"")) #t)) - (add-before 'configure 'autoconf + (add-after 'fix-includes 'autoconf (lambda _ (zero? (system* "autoconf"))))))) (native-inputs `(("autoconf" ,autoconf) @@ -4486,7 +4486,7 @@ distribution, coverage uniformity, strand specificity, etc.") "Data2DB" "PCL2Bin"))) (modify-phases %standard-phases - (add-before 'configure 'bootstrap + (add-after 'unpack 'bootstrap (lambda _ (zero? (system* "bash" "gen_auto")))) (add-after 'build 'build-additional-tools @@ -6164,8 +6164,8 @@ track. The database is exposed as a @code{TxDb} object.") (arguments `(#:phases (modify-phases %standard-phases - (add-before 'configure 'autogen - (lambda _ (zero? (system* "autoreconf" "-vif"))))))) + (add-after 'unpack 'autogen + (lambda _ (zero? (system* "autoreconf" "-vif"))))))) (inputs `(("zlib" ,zlib) ("bzip2" ,bzip2) @@ -8381,14 +8381,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") AC_DEFINE([PLD_png], [1], [Define to 1 if PNG support is available]) AM_CONDITIONAL(AMPNG, true)")) #t)) - (add-after 'unpack 'disable-update-check + (add-after 'fix-checks 'disable-update-check (lambda _ ;; At build time there is no connection to the Internet, so ;; looking for updates will not work. (substitute* "Makefile.am" (("\\$\\(bindir\\)/embossupdate") "")) #t)) - (add-before 'configure 'autogen + (add-after 'disable-update-check 'autogen (lambda _ (zero? (system* "autoreconf" "-vif"))))))) (inputs `(("perl" ,perl) @@ -9453,7 +9453,7 @@ problems in genomics, brain imaging, astrophysics, and data mining.") (substitute-keyword-arguments (package-arguments htslib) ((#:phases phases) `(modify-phases ,phases - (add-before 'configure 'bootstrap + (add-after 'unpack 'bootstrap (lambda _ (zero? (system* "autoreconf" "-vif")))))))) (native-inputs |