diff options
| author | Andreas Tille <tille@debian.org> | 2021-09-09 08:01:13 +0200 |
|---|---|---|
| committer | Andreas Tille <tille@debian.org> | 2021-09-09 08:01:13 +0200 |
| commit | c5a639888ae466cc70164767745f20f3102a6296 (patch) | |
| tree | 7ccfa4e8e624a0cdaca8b27e1ed0c7009fb1dd0c | |
Import rsem_1.3.3+dfsg-2.debian.tar.xz
[dgit import tarball rsem 1.3.3+dfsg-2 rsem_1.3.3+dfsg-2.debian.tar.xz]
| -rw-r--r-- | README.test | 14 | ||||
| -rw-r--r-- | changelog | 138 | ||||
| -rw-r--r-- | clean | 2 | ||||
| -rw-r--r-- | control | 50 | ||||
| -rw-r--r-- | copyright | 32 | ||||
| -rw-r--r-- | dirs | 1 | ||||
| -rw-r--r-- | examples/mouse_ref_building_from_transcripts.tar.gz | bin | 0 -> 35665587 bytes | |||
| -rw-r--r-- | install | 4 | ||||
| -rw-r--r-- | patches/2to3.patch | 180 | ||||
| -rw-r--r-- | patches/hardening | 20 | ||||
| -rw-r--r-- | patches/series | 3 | ||||
| -rw-r--r-- | patches/use_debian_packaged_samtools.patch | 74 | ||||
| -rw-r--r-- | rsem.docs | 7 | ||||
| -rw-r--r-- | rsem.examples | 2 | ||||
| -rw-r--r-- | rsem.manpages | 1 | ||||
| -rwxr-xr-x | rules | 35 | ||||
| -rw-r--r-- | salsa-ci.yml | 4 | ||||
| -rw-r--r-- | source/format | 1 | ||||
| -rw-r--r-- | source/include-binaries | 2 | ||||
| -rw-r--r-- | tests/control | 4 | ||||
| -rw-r--r-- | tests/run-unit-test | 21 | ||||
| -rw-r--r-- | upstream/metadata | 27 | ||||
| -rw-r--r-- | watch | 4 |
23 files changed, 626 insertions, 0 deletions
diff --git a/README.test b/README.test new file mode 100644 index 0000000..a13cde2 --- /dev/null +++ b/README.test @@ -0,0 +1,14 @@ +Notes on how this package can be tested. + + +This package can be tested by executing + + sh run-unit-test + +in order to confirm its integrity. + +Note: The sample data are obtained via + + wget -q https://www.dropbox.com/s/ie67okalzaw8zzj/mouse_ref_building_from_transcripts.tar.gz?dl=0 -O debian/examples/mouse_ref_building_from_transcripts.tar.gz + +More examples and datasets can be found at https://github.com/bli25ucb/RSEM_tutorial diff --git a/changelog b/changelog new file mode 100644 index 0000000..49ba879 --- /dev/null +++ b/changelog @@ -0,0 +1,138 @@ +rsem (1.3.3+dfsg-2) unstable; urgency=medium + + [ Steffen Moeller ] + * Fix watchfile to detect new versions on github (routine-update) + + [ Andreas Tille ] + * Standards-Version: 4.6.0 (routine-update) + * debhelper-compat 13 (routine-update) + * Add salsa-ci file (routine-update) + * Rules-Requires-Root: no (routine-update) + * Use secure URI in Homepage field. + * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, + Repository-Browse. + + -- Andreas Tille <tille@debian.org> Thu, 09 Sep 2021 08:01:13 +0200 + +rsem (1.3.3+dfsg-1) unstable; urgency=medium + + * Update homepage + * New upstream version, added hisat2 mode + * Standards-Version: 4.5.0 (routine-update) + + -- Michael R. Crusoe <michael.crusoe@gmail.com> Mon, 17 Feb 2020 15:49:34 +0100 + +rsem (1.3.2+dfsg-2) unstable; urgency=medium + + * Use 2to3 to port to Python3 + Closes: #938415 + * debhelper-compat 12 + + -- Andreas Tille <tille@debian.org> Thu, 12 Sep 2019 11:39:48 +0200 + +rsem (1.3.2+dfsg-1) unstable; urgency=medium + + * New upstream version + * debhelper 12 + * Standards-Version: 4.4.0 + * Remove trailing whitespace in debian/changelog + + -- Andreas Tille <tille@debian.org> Fri, 12 Jul 2019 21:52:15 +0200 + +rsem (1.3.1+dfsg-1) unstable; urgency=medium + + * New upstream version + * Standards-Version: 4.2.1 + * Fix Perl interpreter path + * Remove unneeded get-orig-source target + + -- Andreas Tille <tille@debian.org> Wed, 26 Sep 2018 21:41:44 +0200 + +rsem (1.3.0+dfsg-2) unstable; urgency=medium + + [ Katerina Kalou ] + * Team upload. + * Add autopkgtest + Closes: #890782 + + [ Andreas Tille ] + * Upload to unstable + Closes: #847569 + * Remove unused lintian-override + * Drop unused License specification + * Point Vcs-fields to Salsa + * Standards-Version: 4.1.4 + + -- Katerina Kalou <aik.kalou@gmail.com> Fri, 25 May 2018 13:56:22 +0200 + +rsem (1.3.0+dfsg-1) experimental; urgency=medium + + * New upstream version + * d/watch: + - version=4 + - xz compression + * remove code copy of samtools-1.3 + * cme fix dpkg-control + * debhelper 11 + * d/rules: do not parse d/changelog + + -- Andreas Tille <tille@debian.org> Sun, 18 Feb 2018 20:34:37 +0100 + +rsem (1.2.31+dfsg-1) unstable; urgency=medium + + * New upstream release + + -- Michael R. Crusoe <michael.crusoe@gmail.com> Sat, 04 Jun 2016 04:40:56 -0700 + +rsem (1.2.30+dfsg-1) unstable; urgency=medium + + * New upstream release + * Use upstream's modified samtools-1.3 as that is required for correct + operation + * re-enable hardening to match source changes + * generate manual pages for rsem-bam2wig & rsem-simulate-reads + + -- Michael R. Crusoe <michael.crusoe@gmail.com> Sun, 15 May 2016 03:49:04 -0700 + +rsem (1.2.26+dfsg-3) unstable; urgency=medium + + * Team upload. + * Bump Standards-Version. + * Enable full hardening. + * Re-introduce bowtie Build-Dep enable builds only on those architectures + where bowtie is available + Closes: #803550 + + -- Sascha Steinbiss <sascha@steinbiss.name> Fri, 13 May 2016 20:45:27 +0000 + +rsem (1.2.26+dfsg-2) unstable; urgency=medium + + * Now compatible with g++-6 (Closes: #811615) + * Section set to 'extra' due to dependency on bowtie|bowtie2 which are both + in section 'extra'. + + -- Michael R. Crusoe <crusoe@ucdavis.edu> Sat, 05 Mar 2016 05:27:01 -0800 + +rsem (1.2.26+dfsg-1) unstable; urgency=medium + + * New upstream release + + -- Michael R. Crusoe <crusoe@ucdavis.edu> Sun, 31 Jan 2016 03:20:22 -0800 + +rsem (1.2.23+dfsg-1) unstable; urgency=medium + + [ Michael R. Crusoe ] + * New upstream release + + [ Andreas Tille ] + * Build-Depends: bowtie to enable builds only on those architectures + where bowtie is available + Closes: #803550 + + -- Michael R. Crusoe <crusoe@ucdavis.edu> Thu, 05 Nov 2015 19:28:01 +0100 + +rsem (1.2.22+dfsg-1) unstable; urgency=low + + * Initial release (Closes: #778578) + + -- Michael R. Crusoe <crusoe@ucdavis.edu> Thu, 27 Aug 2015 13:17:53 -0400 @@ -0,0 +1,2 @@ +debian/*.1 +samtools-1.3/config.mk @@ -0,0 +1,50 @@ +Source: rsem +Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> +Uploaders: Michael R. Crusoe <crusoe@debian.org>, + Andreas Tille <tille@debian.org> +Section: science +Priority: optional +Build-Depends: debhelper-compat (= 13), + zlib1g-dev, + libncurses5-dev, + libboost-dev, + perl <!nocheck>, + python3:any, + help2man, + libhts-dev, + hisat2 <!nocheck>, +# bowtie is a run-time dependency available on only a few systems, not actually +# needed for building but it prevents the creation of uninstallable packages + bowtie | bowtie2 +Standards-Version: 4.6.0 +Vcs-Browser: https://salsa.debian.org/med-team/rsem +Vcs-Git: https://salsa.debian.org/med-team/rsem.git +Homepage: https://deweylab.github.io/RSEM/ +Rules-Requires-Root: no + +Package: rsem +Architecture: any +Depends: ${shlibs:Depends}, + ${misc:Depends}, + ${perl:Depends}, + r-base-core, + bowtie | bowtie2, + python3 +Suggests: r-bioc-ebseq, hisat2 +Description: RNA-Seq by Expectation-Maximization + RSEM is a software package for estimating gene and isoform expression + levels from RNA-Seq data. The RSEM package provides an user-friendly + interface, supports threads for parallel computation of the EM + algorithm, single-end and paired-end read data, quality scores, + variable-length reads and RSPD estimation. In addition, it provides + posterior mean and 95% credibility interval estimates for expression + levels. For visualization, It can generate BAM and Wiggle files in both + transcript-coordinate and genomic-coordinate. Genomic-coordinate files + can be visualized by both UCSC Genome browser and Broad Institute’s + Integrative Genomics Viewer (IGV). Transcript-coordinate files can be + visualized by IGV. RSEM also has its own scripts to generate transcript + read depth plots in pdf format. The unique feature of RSEM is, the read + depth plots can be stacked, with read depth contributed to unique reads + shown in black and contributed to multi-reads shown in red. In addition, + models learned from data can also be visualized. Last but not least, + RSEM contains a simulator. diff --git a/copyright b/copyright new file mode 100644 index 0000000..183c856 --- /dev/null +++ b/copyright @@ -0,0 +1,32 @@ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: RSEM +Source: http://deweylab.biostat.wisc.edu/rsem/src/ +Files-Excluded: boost + EBSeq/*.tar.gz + samtools-1.3 + +Files: * +Copyright: (c) 2009-2015 Bo Li bli25 [at] berkeley [dot] edu +License: GPL-3 + +Files: debian/* +Copyright: (c) 2015 Michigan State University + (c) 2016 Michael R. Crusoe +License: GPL-3 + +License: GPL-3 + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, version 3 of the License. + . + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + . + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + . + On Debian systems, the full text of the GNU General Public + License version 3 can be found in the file + `/usr/share/common-licenses/GPL-3'. @@ -0,0 +1 @@ +usr/bin diff --git a/examples/mouse_ref_building_from_transcripts.tar.gz b/examples/mouse_ref_building_from_transcripts.tar.gz Binary files differnew file mode 100644 index 0000000..509a663 --- /dev/null +++ b/examples/mouse_ref_building_from_transcripts.tar.gz @@ -0,0 +1,4 @@ +# For whatever reason the following scripts are not installed by the upstream install target +rsem-control-fdr usr/bin +rsem-generate-ngvector usr/bin +rsem_perl_utils.pm usr/share/perl5 diff --git a/patches/2to3.patch b/patches/2to3.patch new file mode 100644 index 0000000..2f73150 --- /dev/null +++ b/patches/2to3.patch @@ -0,0 +1,180 @@ +Description: Use 2to3 to port to Python3 +Bug-Debian: https://bugs.debian.org/938415 +Author: Andreas Tille <tille@debian.org> +Last-Update: Thu, 12 Sep 2019 11:26:11 +0200 + +--- a/pRSEM/Gene.py ++++ b/pRSEM/Gene.py +@@ -124,7 +124,7 @@ def constructGenesFromTranscripts(transc + genes = [] + gene_dict_id = {} + for tr in transcripts: +- if gene_dict_id.has_key(tr.gene_id): ++ if tr.gene_id in gene_dict_id: + gene_dict_id[tr.gene_id].transcripts.append(tr) + tr.gene = gene_dict_id[tr.gene_id] + else: +@@ -137,7 +137,7 @@ def constructGenesFromTranscripts(transc + gene_dict_id[tr.gene_id] = gene + tr.gene = gene + +- map(lambda gene: gene.getStartEndTSSTESFromTranscripts(), genes); ++ list(map(lambda gene: gene.getStartEndTSSTESFromTranscripts(), genes)); + + return genes; + +--- a/pRSEM/Param.py ++++ b/pRSEM/Param.py +@@ -98,7 +98,7 @@ class Param: + + + def __str__(self): +- ss = [ "%-33s %s\n" % (key, val) for (key, val) in self.argdict.items()] + \ ++ ss = [ "%-33s %s\n" % (key, val) for (key, val) in list(self.argdict.items())] + \ + [ "%-33s %s\n" % ('RSEM_temp_dir', self.temp_dir ) ] + \ + [ "%-33s %s\n" % ('pRSEM_scr_dir', self.prsem_scr_dir) ] + return ''.join(ss) +@@ -109,7 +109,7 @@ class Param: + import os + prm = cls() + prm.argdict = argdict +- for (key, val) in argdict.items(): ++ for (key, val) in list(argdict.items()): + setattr(prm, key, val) + + if prm.imd_name is not None: +--- a/pRSEM/Prsem.py ++++ b/pRSEM/Prsem.py +@@ -1,4 +1,4 @@ +-#!/bin/env python ++#!/usr/bin/python3 + + __doc__=""" + +@@ -65,9 +65,9 @@ def buildTrainingSet(prm): + The order is required by rsem-run-gibbs so that prior can be assigned to + transcript correctly + """ +- ogot_genes = filter(lambda g: len(g.transcripts) == 1 and ++ ogot_genes = [g for g in prm.genes if len(g.transcripts) == 1 and + (g.end - g.start + 1) >= +- prm.TRAINING_GENE_MIN_LEN, prm.genes) ++ prm.TRAINING_GENE_MIN_LEN] + + trs = [tr for g in ogot_genes for tr in g.transcripts] + +@@ -127,7 +127,7 @@ def genPriorByCombinedTSSSignals(prm): + """ + f_fout = open(prm.finfo_multi_targets, 'w') + f_fout.write("targetid\tfaln\tfftrs\n") +- for (tgtid, faln) in prm.targetid2fchipseq_alignment.items(): ++ for (tgtid, faln) in list(prm.targetid2fchipseq_alignment.items()): + fftrs = prm.imd_name + '_prsem.' + tgtid + '.all_tr_features' + f_fout.write("%s\t%s\t%s\n" % (tgtid, faln, fftrs)) + f_fout.close() +--- a/pRSEM/Transcript.py ++++ b/pRSEM/Transcript.py +@@ -41,7 +41,7 @@ class Transcript: + for (start, end) in self.exon_ranges: + s += " %d %d" % (start, end); + s += "\n"; +- for key in self.gtf_attr.keys(): ++ for key in list(self.gtf_attr.keys()): + for val in self.gtf_attr[key]: + s += '%s "%s"; ' % (key, val); + s = s.rstrip(); +@@ -58,7 +58,7 @@ class Transcript: + for feature_word in feature_words: + feature_word.lstrip(); + (key, val) = feature_word.split(); +- if not self.gtf_attr.has_key(key): ++ if key not in self.gtf_attr: + self.gtf_attr[key] = []; + self.gtf_attr[key].append(val.strip('"')); + +@@ -160,7 +160,7 @@ def readRSEMTI(fin): + tr.constructFromRSEMTI(lines[i*6+1:i*6+7]); + transcripts.append(tr); + if (i > 0) and (i % 20000 == 0): +- print "processed %d transcripts" % i; ++ print("processed %d transcripts" % i); + + return transcripts; + +@@ -183,7 +183,7 @@ def quicklyReadRSEMTI(fin): + tr.quicklyConstructFromRSEMTI(lines[i*6+1:i*6+7]); + transcripts.append(tr); + if (i > 0) and (i % 20000 == 0): +- print "processed %d transcripts" % i; ++ print("processed %d transcripts" % i); + + return transcripts; + +--- a/pRSEM/Util.py ++++ b/pRSEM/Util.py +@@ -60,7 +60,7 @@ def runCommandAndGetOutput(*args, **kwar + + try: + output = subprocess.check_output(str_args) +- except subprocess.CalledProcessError, e: ++ except subprocess.CalledProcessError as e: + sys.exit("\nExecution failed: %s\n" % e.output) + + return output +@@ -123,14 +123,14 @@ def runMPOverAList(nprocs, func, args): + if len(args[0]) > nprocs: + chunksize = len(args[0])/nprocs + 1 + procs = [] +- for i in xrange(nprocs): ++ for i in range(nprocs): + list_args = [args[0][chunksize*i:chunksize*(i+1)]] + args[1:] + [out_q] + p = mp.Process(target = func, args = tuple(list_args)) + procs.append(p) + p.start() + + dict_to_return = {} +- for i in xrange(nprocs): ++ for i in range(nprocs): + dict_to_return.update(out_q.get()) + + for p in procs: +--- a/pRSEM/prsem-calculate-expression ++++ b/pRSEM/prsem-calculate-expression +@@ -1,4 +1,4 @@ +-#!/bin/env python ++#!/usr/bin/python3 + + __doc__=""" + +--- a/pRSEM/prsem-prepare-reference ++++ b/pRSEM/prsem-prepare-reference +@@ -1,4 +1,4 @@ +-#!/bin/env python ++#!/usr/bin/python3 + + __doc__=""" + +--- a/pRSEM/prsem-testing-procedure ++++ b/pRSEM/prsem-testing-procedure +@@ -1,4 +1,4 @@ +-#!/bin/env python ++#!/usr/bin/python3 + + __doc__=""" + +--- a/rsem-gff3-to-gtf ++++ b/rsem-gff3-to-gtf +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python3 + + # Copyright (c) 2016 + # Bo Li (University of California, Berkeley) +--- a/rsem-refseq-extract-primary-assembly ++++ b/rsem-refseq-extract-primary-assembly +@@ -1,4 +1,4 @@ +-#!/usr/bin/env python ++#!/usr/bin/python3 + + from sys import argv, exit + diff --git a/patches/hardening b/patches/hardening new file mode 100644 index 0000000..a297f00 --- /dev/null +++ b/patches/hardening @@ -0,0 +1,20 @@ +Author: Michael R. Crusoe <michael.crusoe@gmail.com> +Description: accept the hardening flags +--- rsem.orig/Makefile ++++ rsem/Makefile +@@ -12,11 +12,11 @@ + + # Compilation variables + CXX = g++ +-CXXFLAGS = -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB) +-CPPFLAGS = ++CXXFLAGS += -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB) ++CPPFLAGS ?= + +-LDFLAGS = +-LDLIBS = ++LDFLAGS ?= ++LDLIBS ?= + + # Installation variables + INSTALL = install diff --git a/patches/series b/patches/series new file mode 100644 index 0000000..edefc32 --- /dev/null +++ b/patches/series @@ -0,0 +1,3 @@ +hardening +use_debian_packaged_samtools.patch +2to3.patch diff --git a/patches/use_debian_packaged_samtools.patch b/patches/use_debian_packaged_samtools.patch new file mode 100644 index 0000000..45f03e4 --- /dev/null +++ b/patches/use_debian_packaged_samtools.patch @@ -0,0 +1,74 @@ +Author: Andreas Tille <tille@debian.org> +Last-Update: Fri, 09 Dec 2016 14:26:08 +0100 +Description: Use Debian packaged samtools + +--- a/Makefile ++++ b/Makefile +@@ -12,7 +12,7 @@ BOOST = . + + # Compilation variables + CXX = g++ +-CXXFLAGS += -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB) ++CXXFLAGS += -std=gnu++98 -Wall -I. -I$(BOOST) + CPPFLAGS ?= + + LDFLAGS ?= +@@ -30,8 +30,8 @@ exec_prefix = $(prefix) + bindir = $(exec_prefix)/bin + + # Auxiliary variables for compilation +-SAMHEADERS = $(SAMTOOLS)/$(HTSLIB)/htslib/sam.h +-SAMLIBS = $(SAMTOOLS)/$(HTSLIB)/libhts.a ++SAMHEADERS = ++SAMLIBS = + CONFIGURE = ./configure + + OBJS1 = parseIt.o +@@ -54,12 +54,12 @@ SCRIPTS = rsem-prepare-reference rsem-ca + + .PHONY : all ebseq pRSEM clean + +-all : $(PROGRAMS) $(SAMTOOLS)/samtools ++all : $(PROGRAMS) + + $(SAMTOOLS)/samtools : + cd $(SAMTOOLS) && $(CONFIGURE) --without-curses && $(MAKE) -f $(SAMTOOLS_MAKEFILE) samtools + +-$(SAMLIBS) : $(SAMTOOLS)/samtools ++$(SAMLIBS) : + + + # Compile objects +@@ -78,10 +78,10 @@ $(PROGS1) : + $(CXX) $(LDFLAGS) -o $@ $^ $(LDLIBS) + + $(PROGS2) : +- $(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) -lz ++ $(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) -lhts -lz + + $(PROGS3) : +- $(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) ++ $(CXX) $(LDFLAGS) -pthread -o $@ $^ $(LDLIBS) -lhts + + + # Dependencies for executables +@@ -163,17 +163,13 @@ pRSEM : + + + # Install RSEM +-install : $(PROGRAMS) $(SCRIPTS) $(SAMTOOLS)/samtools rsem_perl_utils.pm +- $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/$(SAMTOOLS) +- $(foreach prog,$(PROGRAMS),$(INSTALL_PROGRAM) $(prog) $(DESTDIR)$(bindir)/$(prog) ; $(STRIP) $(DESTDIR)$(bindir)/$(prog) ;) +- $(INSTALL_PROGRAM) $(SAMTOOLS)/samtools $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools +- $(STRIP) $(DESTDIR)$(bindir)/$(SAMTOOLS)/samtools ++install : $(PROGRAMS) $(SCRIPTS) rsem_perl_utils.pm ++ $(foreach prog,$(PROGRAMS),$(INSTALL_PROGRAM) $(prog) $(DESTDIR)$(bindir)/$(prog) ; ) + $(foreach script,$(SCRIPTS),$(INSTALL_PROGRAM) $(script) $(DESTDIR)$(bindir)/$(script) ;) + $(INSTALL_DATA) rsem_perl_utils.pm $(DESTDIR)$(bindir)/rsem_perl_utils.pm + + # Clean + clean : + rm -f *.o *~ $(PROGRAMS) +- cd $(SAMTOOLS) && $(MAKE) clean-all + cd EBSeq && $(MAKE) clean + cd pRSEM && $(MAKE) clean diff --git a/rsem.docs b/rsem.docs new file mode 100644 index 0000000..40cb8d4 --- /dev/null +++ b/rsem.docs @@ -0,0 +1,7 @@ +README.md +debian/README.test +WHAT_IS_NEW +cnt_file_description.txt +model_file_description.txt +debian/tests/run-unit-test + diff --git a/rsem.examples b/rsem.examples new file mode 100644 index 0000000..cf6e7e7 --- /dev/null +++ b/rsem.examples @@ -0,0 +1,2 @@ +debian/examples/* + diff --git a/rsem.manpages b/rsem.manpages new file mode 100644 index 0000000..0f65186 --- /dev/null +++ b/rsem.manpages @@ -0,0 +1 @@ +debian/*.1 @@ -0,0 +1,35 @@ +#!/usr/bin/make -f + +DH_VERBOSE := 1 + +include /usr/share/dpkg/default.mk + +export DEB_BUILD_MAINT_OPTIONS=hardening=+all + +%: + dh $@ + +override_dh_auto_build: + dh_auto_build -- BOOST=/usr/include prefix=debian/tmp + for prog in convert-sam-for-rsem rsem-calculate-expression \ + rsem-control-fdr rsem-generate-ngvector \ + rsem-plot-transcript-wiggles rsem-prepare-reference \ + rsem-run-ebseq; do pod2man $${prog} debian/$${prog}.1; done + help2man ./rsem-gff3-to-gtf --no-info --version-string="$(DEB_VERSION_UPSTREAM)" \ + --name 'Convert GFF3 files to GTF files.' > \ + debian/rsem-gff3-to-gtf.1 + help2man ./rsem-bam2wig --no-info --version-string="$(DEB_VERSION_UPSTREAM)" \ + --name 'Convert BAM files to wiggle files.' > \ + debian/rsem-bam2wig.1 + help2man ./rsem-simulate-reads --no-info --version-string="$(DEB_VERSION_UPSTREAM)" \ + --name 'Simulate RNA-Seq data ("reads") for a given model and a RSEM reference transcript collection.' > \ + debian/rsem-simulate-reads.1 + +override_dh_auto_install: + dh_auto_install -- BOOST=/usr/include prefix="/usr" + +override_dh_install: + dh_install + for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ + sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \ + done diff --git a/salsa-ci.yml b/salsa-ci.yml new file mode 100644 index 0000000..33c3a64 --- /dev/null +++ b/salsa-ci.yml @@ -0,0 +1,4 @@ +--- +include: + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml diff --git a/source/format b/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/source/include-binaries b/source/include-binaries new file mode 100644 index 0000000..f6782bc --- /dev/null +++ b/source/include-binaries @@ -0,0 +1,2 @@ +debian/examples/mouse_ref_building_from_transcripts.tar.gz + diff --git a/tests/control b/tests/control new file mode 100644 index 0000000..f2c3b32 --- /dev/null +++ b/tests/control @@ -0,0 +1,4 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr + diff --git a/tests/run-unit-test b/tests/run-unit-test new file mode 100644 index 0000000..23039ab --- /dev/null +++ b/tests/run-unit-test @@ -0,0 +1,21 @@ +#!/bin/bash +set -e +set -x + +pkg="rsem" + + +if [ "$AUTOPKGTEST_TMP" = "" ] ; then + AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX` + trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM +fi + +cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP + +cd $AUTOPKGTEST_TMP + +tar -C . -xzf *.tar.gz + +rsem-prepare-reference \ + --transcript-to-gene-map mouse_ref_mapping.txt \ + mouse_ref.fa mouse_ref diff --git a/upstream/metadata b/upstream/metadata new file mode 100644 index 0000000..8ff6ac2 --- /dev/null +++ b/upstream/metadata @@ -0,0 +1,27 @@ +Bug-Database: https://github.com/bli25wisc/rsem/issues +Bug-Submit: https://github.com/bli25wisc/rsem/issues/new +Reference: + Author: Li, Bo and Dewey, Colin + Title: > + RSEM: accurate transcript quantification from RNA-Seq data with + or without a reference genome + Journal: BMC Bioinformatics + Year: 2011 + Volume: 12 + Number: 1 + Pages: 323 + DOI: 10.1186/1471-2105-12-323 + PMID: 21816040 + URL: http://www.biomedcentral.com/1471-2105/12/323 + eprint: http://www.biomedcentral.com/content/pdf/1471-2105-12-323.pdf +Registry: + - Name: OMICtools + Entry: OMICS_01287 + - Name: bio.tools + Entry: rsem + - Name: SciCrunch + Entry: SCR_013027 + - Name: conda:bioconda + Entry: rsem +Repository: https://github.com/bli25wisc/rsem.git +Repository-Browse: https://github.com/bli25wisc/rsem @@ -0,0 +1,4 @@ +version=4 + +opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \ + https://github.com/bli25wisc/rsem/tags (?:.*?/)?v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) |