gnu: Fix build failures caused by commit
d10092b849153dc27cfed0a9601fde6c7bdec918.

* gnu/packages/bioinformatics.scm (seek)[arguments]: Restore previous phase
order.
* gnu/packages/ci.scm (cuirass)[arguments]: Add patch-/bin/sh phase.

gnu: Add r-sparql.

* gnu/packages/bioinformatics.scm (r-sparql): New variable.

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.

gnu: r-genomicalignments: Update to 1.12.2.

* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.12.2.

gnu: r-vegan: Update to 2.4-4.

* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-4.
[native-inputs]: Remove r-knitr.

gnu: r-maldiquant: Update to 1.16.4.

* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.16.4.

gnu: r-bookdown: Update to 0.5.

* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.5.

gnu: r-rcas: Correct license.

* gnu/packages/bioinformatics.scm (r-rcas)[license]: Use correct license.

gnu: r-rcas: Update to 1.3.3.

* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.3.3.

gnu: vsearch: Update to 2.4.4.

* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.4.

gnu: metabat: Update to 2.12.1.

* gnu/packages/patches/metabat-remove-compilation-date.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/bioinformatics.scm (metabat): Update to 2.12.1.
[source]: Remove it.  Use url-fetch.

gnu: bioinformatics: Work around more "dotless @INC" build failures.

* gnu/packages/bioinformatics.scm (ncbi-vdb, sra-tools)[arguments]: Add
'set-perl-search-path' phase.

gnu: metabat: Update to 2.11.3.

* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.3.
[source]: Use git-fetch.  Remove boost-related patch.
* gnu/packages/patches/metabat-fix-boost-issue.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.

gnu: multiqc: Update to 1.2.

* gnu/packages/bioinformatics.scm (multiqc): Update to 1.2.
[source]: Remove patches.
[arguments]: Remove to enable tests.
[propagated-inputs]: Add python-spectra, python-requests, python-markdown,
python-lzstring.
* gnu/packages/patches/multiqc-fix-git-subprocess-error.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.

Merge branch 'core-updates'

Merge branch 'master' into core-updates

gnu: Add r-annotationfilter.

* gnu/packages/bioinformatics.scm (r-annotationfilter): New variable.

gnu: Add r-methylkit.

* gnu/packages/bioinformatics.scm (r-methylkit): New variable.

gnu: Add r-qvalue.

* gnu/packages/bioinformatics.scm (r-qvalue): New variable.

gnu: Add r-fastseg.

* gnu/packages/bioinformatics.scm (r-fastseg): New variable.