gnu: bowtie: Use 'modify-phases'.

* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Use 'modify-phases'
syntax.

gnu: bowtie: Update to 2.3.2.

* gnu/packages/bioinformatics.scm (bowtie): Update to 2.3.2.
[inputs]: Add zlib.

gnu: deeptools: Update to 2.5.1.

* gnu/packages/bioinformatics.scm (deeptools): Update to 2.5.1.
[arguments]: Remove.
[native-inputs]: Use "python-" instead of "python2-" variants.
[inputs]: Likewise; add python-py2bit.

gnu: Add python-py2bit.

* gnu/packages/bioinformatics.scm (python-py2bit): New variable.

gnu: blast+: Update to 2.6.0.

* gnu/packages/bioinformatics.scm (blast+): Update to 2.6.0.
[origin]: Remove bundled pcre.  Add patch.
[arguments]: Replace paths in run_with_lock.c.  Configure with pcre.
[inputs]: Add pcre, perl, python.
* gnu/packages/patches/blast+-fix-makefile.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.

Revert "gnu: blast+: Update to 2.6.0."

This reverts commit 18dea67dc3a42d782b34b551304748346f173184.

gnu: gemma: Fix building on non-Intel architectures.

* gnu/packages/patches/gemma-intel-compat.patch: New file.
* gnu/packages/bioinformatics.scm (gemma)[source]: Add patch.
[arguments]: Add NO_INTEL_COMPAT flag on non-Intel architectures.
* gnu/local.mk (dist_patch_DATA): Register patch.

gnu: diamond: Update to 0.9.9.

* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.9.

gnu: blast+: Update to 2.6.0.

* gnu/packages/bioinformatics.scm (blast+): Update to 2.6.0.
[origin]: Remove bundled pcre.
[arguments]: Replace paths in run_with_lock.c.  Configure with pcre.
[inputs]: Add pcre, perl, python.

gnu: cd-hit: Update to 4.6.8.

* gnu/packages/bioinformatics.scm (cd-hit): Update to 4.6.8.

gnu: bwa: Update to 0.7.15.

* gnu/packages/bioinformatics.scm (bwa): Update to 0.7.15.

gnu: Add f-seq.

* gnu/packages/bioinformatics.scm (f-seq): New variable.

gnu: orfm: Update to 0.7.1.

* gnu/packages/bioinformatics.scm (orfm): Update to 0.7.1.

gnu: orfm: Update to 0.7.0.

* gnu/packages/bioinformatics.scm (orfm): Update to 0.7.0.

gnu: Add kentutils.

* gnu/packages/bioinformatics.scm (kentutils): New variable.

gnu: python2-bx-python: Update to 0.7.3.

* gnu/packages/bioinformatics.scm (python2-bx-python): Update to 0.7.3.

gnu: Move contents of zip module into compression module.

* gnu/packages/zip.scm (zip, unzip, zziplib, perl-zip): Move to...
* gnu/packages/compression.scm: ...here.
* gnu/packages/zip.scm: Delete file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Unregister deleted file.
* po/packages/POTFILES.in: Unregister deleted file.
* gnu/packages/{audio, avr, bioinformatics, busybox, cdrom, ci, compression,
docbook, documentation, fonts, fpga, game-development, games, gl, gnome,
gnuzilla, graphics, guile, haskell, image, java, kodi, ldc, libreoffice,
markup, maths, mc, monitoring, music, php, pretty-print, python, scheme,
smalltalk, statistics, synergy, tex, textutils, video, web-browsers, xml,
zip}.scm, guix/build-system/{ant, font}.scm, guix/{download, packages}.scm:
Adapt module import.

gnu: diamond: Update to 0.9.8.

* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.8.

gnu: tadbit: Fix typo in description.

* gnu/packages/bioinformatics.scm (tadbit)[description]: Fix typo.

gnu: gemma: Fix indentation.

* gnu/packages/bioinformatics.scm (gemma)[arguments]: Fix indentation.