[med-svn] [Git][med-team/drop-seq][master] 8 commits: Reverting some parts of commit 32a75df6acc1ff6eabb6a032bab0708e93081c3f
Pierre Gruet
gitlab at salsa.debian.org
Fri Feb 12 21:55:01 GMT 2021
Pierre Gruet pushed to branch master at Debian Med / drop-seq
Commits:
b91ac10e by Pierre Gruet at 2021-02-12T21:36:38+01:00
Reverting some parts of commit 32a75df6acc1ff6eabb6a032bab0708e93081c3f
This commit had changed files by applying patches, which is certainly not
expected.
- - - - -
e0df858f by Pierre Gruet at 2021-02-12T21:45:25+01:00
Forwarding the patches is not needed
- - - - -
7d6de841 by Pierre Gruet at 2021-02-12T22:49:14+01:00
Marking drop-seq-testdata as Multi-Arch: foreign
- - - - -
0936e1c3 by Pierre Gruet at 2021-02-12T22:49:48+01:00
Adding two manpages
Hacking in d/rules so that "classic" man pages are installed even if the
extension of the executable files is .sh
- - - - -
91d6399d by Pierre Gruet at 2021-02-12T22:51:06+01:00
Adding a lintian override for executables with extension .sh
- - - - -
4672702b by Pierre Gruet at 2021-02-12T22:51:42+01:00
Setting the classpath properly in d/drop-seq-tools.manifest
- - - - -
b57086da by Pierre Gruet at 2021-02-12T22:52:22+01:00
Setting the path /usr/share/java for jars in the executable scripts
- - - - -
3669e5a1 by Pierre Gruet at 2021-02-12T22:54:47+01:00
Updating changelog
- - - - -
15 changed files:
- README.md
- debian/changelog
- debian/control
- + debian/drop-seq-tools.lintian-overrides
- + debian/drop-seq-tools.manifest
- + debian/drop-seq-tools.manpages
- + debian/man/Drop-seq_alignment.sh.1
- + debian/man/create_Drop-seq_reference_metadata.sh.1
- debian/patches/debian_packaged_libs.patch
- debian/patches/link_excluded_file.patch
- debian/patches/no_git.patch
- + debian/patches/paths_in_scripts.patch
- debian/patches/series
- debian/rules
- src/ant/defs.xml
Changes:
=====================================
README.md
=====================================
@@ -6,6 +6,6 @@ You may also use this address to be added to the Drop-seq Google group.
See https://github.com/broadinstitute/Drop-seq/releases to download binaries.
-See [Drop-seq alignment cookbook](https://github.com/broadinstitute/Drop-seq/blob/master/doc/Drop-seq_Alignment_Cookbook.pdf) for detailed usage of these tools.
+See [Drop-seq alignment cookbook](doc/Drop-seq_Alignment_Cookbook.pdf) for detailed usage of these tools.
-See [Census-seq computational protocols](doc/Census-seq_Computational_Protcools.pdf) for detailed usage of Census-Seq tools.
+See [Census-seq computational protocols](doc/Census-seq_Computational_Protcools.pdf) for detailed usage of Census-Seq tools.
\ No newline at end of file
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+drop-seq (2.4.0+dfsg-6) UNRELEASED; urgency=medium
+
+ * Team upload
+ * Properly specify classpath in d/drop-seq-tools.manifest (Closes: #982617)
+ * Setting the correct Debian path for jars in the executable shell scripts
+ * Adding two manpages
+ * Adding a lintian override for .sh executable files
+ * Marking drop-seq-testdata as Multi-Arch: foreign
+ * Reverting some parts of commit 32a75df6acc1ff6eabb6a032bab0708e93081c3f
+ which committed contents with applied patches
+
+ -- Pierre Gruet <pgtdebian at free.fr> Fri, 12 Feb 2021 22:52:38 +0100
+
drop-seq (2.4.0+dfsg-5) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -43,6 +43,7 @@ Description: analyzing Drop-seq data
Package: drop-seq-testdata
Architecture: all
Depends: ${misc:Depends}
+Multi-Arch: foreign
Description: analyzing Drop-seq data (testdata)
This software provide for core computational analysis of Drop-seq data,
which shows you how to transform raw sequence data into an expression
=====================================
debian/drop-seq-tools.lintian-overrides
=====================================
@@ -0,0 +1,2 @@
+# see https://lists.debian.org/debian-med/2018/06/msg00043.html
+script-with-language-extension usr/bin/*.sh
=====================================
debian/drop-seq-tools.manifest
=====================================
@@ -0,0 +1,3 @@
+usr/share/java/dropseq.jar:
+ Main-Class: org.broadinstitute.dropseqrna.cmdline.DropSeqMain
+ Class-Path: /usr/share/java/guava.jar /usr/share/java/gson.jar /usr/share/java/htsjdk.jar /usr/share/java/picard.jar /usr/share/java/commons-collections4.jar /usr/share/java/commons-io.jar /usr/share/java/commons-lang.jar /usr/share/java/commons-math3.jar /usr/share/java/barclay.jar /usr/share/java/la4j.jar /usr/share/java/snakeyaml.jar
=====================================
debian/drop-seq-tools.manpages
=====================================
@@ -0,0 +1,2 @@
+debian/man/create_Drop-seq_reference_metadata.sh.1
+debian/man/Drop-seq_alignment.sh.1
=====================================
debian/man/Drop-seq_alignment.sh.1
=====================================
@@ -0,0 +1,32 @@
+.TH DROP-SEQ_ALIGNMENT.SH "1" "February 2021" "Drop-seq_alignment.sh" "User Commands"
+.SH NAME
+Drop-seq_alignment.sh \- perform Drop\-seq tagging, trimming and alignment
+.SH DESCRIPTION
+USAGE: Drop\-seq_alignment.sh [options] <unmapped\-queryname\-sorted.bam>
+.SS OPTIONS
+.PP
+\fB\-g\fR <genomedir>
+Directory of STAR genome directory. Required.
+.TP
+\fB\-r\fR <referencefasta>
+Reference fasta of the Drop\-seq reference metadata bundle. Required.
+.TP
+\fB\-d\fR <dropseq_root>
+Directory containing Drop\-seq executables. Default: directory containing this script.
+.TP
+\fB\-o\fR <outputdir>
+Where to write output bam. Default: current directory.
+.TP
+\fB\-t\fR <tmpdir>
+Where to write temporary files. Default: a new subdirectory in .
+.TP
+\fB\-s\fR <STAR_path>
+Full path of STAR. Default: STAR is found via PATH environment variable.
+.TP
+\fB\-e\fR
+Echo commands instead of executing them.
+.TP
+\fB\-k\fR
+Keep intermediate files
+.SH "SEE ALSO"
+\fBcreate_Drop-seq_reference_metadata.sh\fR(1)
=====================================
debian/man/create_Drop-seq_reference_metadata.sh.1
=====================================
@@ -0,0 +1,50 @@
+.TH CREATE_DROP-SEQ_REFERENCE_METADATA.SH "1" "February 2021" "create_Drop-seq_reference_metadata.sh" "User Commands"
+.SH NAME
+create_Drop-seq_reference_metadata.sh \- create Drop\-seq reference metadata bundle
+.SH DESCRIPTION
+USAGE: create_Drop\-seq_reference_metadata.sh [options]
+.SS OPTIONS
+.PP
+\fB\-n\fR <name>
+Name for reference metadata set to be created. Required.
+.TP
+\fB\-r\fR <referencefasta>
+Reference fasta of the Drop\-seq reference metadata bundle. Required.
+.TP
+\fB\-s\fR <species>
+Species. Required.
+.TP
+\fB\-g\fR <gtf>
+Gene annotation file. Required.
+.TP
+\fB\-f\fR <filtered\-gene\-biotype>
+Annotations with the given gene_biotype will be filtered. Multiple values may be
+specified by using this argument more than once, and/or by providing a comma\-separated list.
+Use ValidateReference command to see the gene_biotypes in your GTF in order to decide what to
+exclude. Default: not gene biotypes are filtered.
+.PP
+\fB\-d\fR <dropseq_root>
+Directory containing Drop\-seq executables. Default: directory containing this script.
+.TP
+\fB\-o\fR <outputdir>
+Where to write output bam. Default: current directory.
+.TP
+\fB\-t\fR <tmpdir>
+Where to write temporary files. Default: Value of 132153TMPDIR environment variable.
+.TP
+\fB\-a\fR <STAR_path>
+Full path of STAR. Default: STAR is found via PATH environment variable.
+.TP
+\fB\-b\fR <bgzip_path>
+Full path of bgzip: Default: bgzip is found via PATH environment variable.
+.TP
+\fB\-i\fR <samtools_path>
+Full path of samtools. Default: samtools is found via PATH environment variable.
+.TP
+\fB\-v\fR
+verbose
+.TP
+\fB\-e\fR
+merely echo commands instead of executing
+.SH "SEE ALSO"
+\fBDrop-seq_alignment.sh\fR(1)
=====================================
debian/patches/debian_packaged_libs.patch
=====================================
@@ -1,6 +1,7 @@
Author: Andreas Tille <tille at debian.org>
Last-Update: Tue, 19 May 2020 14:42:01 +0200
Description: Use Debian packaged Java libs
+Forwarded: not-needed
--- a/src/ant/defs.xml
+++ b/src/ant/defs.xml
=====================================
debian/patches/link_excluded_file.patch
=====================================
@@ -2,6 +2,7 @@ Author: Steffen Moeller
Last-Update: 2020-09-20 20:21:32 +0200
Description: The PDF documentation had to be excluded as binary without source
This patch links to the online version
+Forwarded: not-needed
Index: drop-seq/README.md
===================================================================
=====================================
debian/patches/no_git.patch
=====================================
@@ -1,6 +1,7 @@
Author: Andreas Tille <tille at debian.org>
Last-Update: Tue, 19 May 2020 14:42:01 +0200
Description: Do not try to run Git
+Forwarded: not-needed
--- a/src/ant/defs.xml
+++ b/src/ant/defs.xml
=====================================
debian/patches/paths_in_scripts.patch
=====================================
@@ -0,0 +1,45 @@
+Description: Putting Debian paths for the jars in .sh executables
+Author: Pierre Gruet <pgtdebian at free.fr>
+Forwarded: not-needed
+Last-Update: 2021-02-12
+
+--- a/src/scripts/Drop-seq_alignment.sh
++++ b/src/scripts/Drop-seq_alignment.sh
+@@ -114,7 +114,7 @@
+ gene_intervals=$(dirname $reference)/$reference_basename.genes.intervals
+ exon_intervals=$(dirname $reference)/$reference_basename.exon.intervals
+ refflat=$(dirname $reference)/$reference_basename.refFlat
+-picard_jar=${dropseq_root}/3rdParty/picard/picard.jar
++picard_jar=/usr/share/java/picard.jar
+
+ unmapped_bam=$1
+ tagged_unmapped_bam=${tmpdir}/unaligned_mc_tagged_polyA_filtered.bam
+--- a/src/scripts/create_Drop-seq_reference_metadata.sh
++++ b/src/scripts/create_Drop-seq_reference_metadata.sh
+@@ -118,7 +118,7 @@
+ }
+
+ function invoke_picard() {
+- check_invoke java -jar $dropseq_root/3rdParty/picard/picard.jar $@
++ check_invoke java -jar /usr/share/java/picard.jar $@
+ }
+
+ function invoke_dropseq() {
+--- a/src/scripts/public_clp_template.sh
++++ b/src/scripts/public_clp_template.sh
+@@ -30,7 +30,7 @@
+ then source $thisdir/loadDotKits.sh
+ fi
+
+-jar_deploy_dir=$thisdir/jar
++jar_deploy_dir=/usr/share/java
+ verbose=0
+
+ USAGE=$(cat << EOF
+@@ -72,4 +72,4 @@
+ then set -x
+ fi
+
+-java -Xmx${xmx} -XX:+UseParallelOldGC -XX:ParallelGCThreads=1 -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:+HeapDumpOnOutOfMemoryError -Djava.io.tmpdir=$TMPDIR -jar $jar_deploy_dir/dropseq.jar $progname $*
+\ No newline at end of file
++java -Xmx${xmx} -XX:+UseParallelOldGC -XX:ParallelGCThreads=1 -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -XX:+HeapDumpOnOutOfMemoryError -Djava.io.tmpdir=$TMPDIR -jar $jar_deploy_dir/dropseq.jar $progname $*
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
no_git.patch
debian_packaged_libs.patch
link_excluded_file.patch
+paths_in_scripts.patch
=====================================
debian/rules
=====================================
@@ -34,3 +34,8 @@ override_dh_auto_clean:
override_dh_fixperms:
dh_fixperms
find debian/drop-seq-testdata/usr/share -type f -exec chmod -x \{\} \;
+
+# Invoking dh_installman with --language=C to get "traditional" manpages
+# although the files we put in /usr/bin end with ".sh".
+override_dh_installman:
+ dh_installman --language=C
=====================================
src/ant/defs.xml
=====================================
@@ -24,6 +24,11 @@
<!-- To be included in build.xml -->
<!-- Get GIT hash, if available, otherwise leave it blank. -->
+<exec executable="git" outputproperty="repository.revision" failifexecutionfails="true" errorproperty="">
+ <arg value="log"/>
+ <arg value="-1"/>
+ <arg value="--pretty=format:%h_%at"/>
+</exec>
<property name="repository.revision" value=""/>
@@ -122,14 +127,12 @@
xmlns:jacoco="antlib:org.jacoco.ant"
to the <project> element in the file where this file is included.
-->
-<!-- jacoco is not packaged for Debianso we can not run this test
<property name="jacoco.dir" location="jacoco_reports"/>
<property name="jacoco.binary" location="${jacoco.dir}/jacoco.exec"/>
<taskdef uri="antlib:org.jacoco.ant" resource="org/jacoco/ant/antlib.xml">
<classpath path="${public.dir}/lib/test/jacocoant.jar"/>
</taskdef>
--->
<!-- Unfortunately can't invoke a macro from inside <jacoco:coverage>, so testng invocation is duplicated -->
<target name="coverage" depends="compile-tests">
@@ -171,7 +174,5 @@
</jacoco:report>
</target>
-<!-- jacoco is not packaged for Debianso we can not run this test
<target name="coverage-and-report" depends="coverage, coverage-report"
description="Run unit test suite with coverage and generate report"/>
--->
View it on GitLab: https://salsa.debian.org/med-team/drop-seq/-/compare/32a75df6acc1ff6eabb6a032bab0708e93081c3f...3669e5a1ae03d97269720e4445c2580949addeda
--
View it on GitLab: https://salsa.debian.org/med-team/drop-seq/-/compare/32a75df6acc1ff6eabb6a032bab0708e93081c3f...3669e5a1ae03d97269720e4445c2580949addeda
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