[med-svn] [subread] 07/08: d/subread.install: remove globalReassembly and subtools, add repair d/rules: generate man page for repair d/patches/fix_repair_usage.patch: s/removeDup/repair/g d/patches/syntax_err.patch: s/requried/required/ d/patches/fix_syntax.patch: removed d/subread.docs: do not install pdf file d/doc-base: removed due to removal of pdf d/control: remove texlive-latex-extra from build-depends d/copyright: remove stanza for non-existing file
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Wed Nov 11 18:07:00 UTC 2015
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a commit to branch master
in repository subread.
commit 266d293ee0f713baf0a5f0eda3322a13c4586b53
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Wed Nov 11 12:49:38 2015 +0100
d/subread.install: remove globalReassembly and subtools, add repair
d/rules: generate man page for repair
d/patches/fix_repair_usage.patch: s/removeDup/repair/g
d/patches/syntax_err.patch: s/requried/required/
d/patches/fix_syntax.patch: removed
d/subread.docs: do not install pdf file
d/doc-base: removed due to removal of pdf
d/control: remove texlive-latex-extra from build-depends
d/copyright: remove stanza for non-existing file
---
debian/control | 2 +-
debian/copyright | 7 -------
debian/doc-base | 12 ------------
debian/patches/fix_repair_usage.patch | 13 +++++++++++++
debian/patches/fix_syntax.patch | 13 -------------
debian/patches/series | 2 ++
debian/patches/syntax_err.patch | 13 +++++++++++++
debian/rules | 2 +-
debian/subread.docs | 1 -
debian/subread.install | 3 +--
10 files changed, 31 insertions(+), 37 deletions(-)
diff --git a/debian/control b/debian/control
index c86358b..efb5288 100644
--- a/debian/control
+++ b/debian/control
@@ -5,7 +5,7 @@ Uploaders: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>,
Section: science
Testsuite: autopkgtest
Priority: optional
-Build-Depends: debhelper (>= 9), help2man, texlive-latex-extra, zlib1g-dev
+Build-Depends: debhelper (>= 9), help2man, zlib1g-dev
Standards-Version: 3.9.6
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/subread.git
Vcs-Git: git://anonscm.debian.org/debian-med/subread.git
diff --git a/debian/copyright b/debian/copyright
index ab76481..e282d99 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -7,10 +7,6 @@ Files: *
Copyright: 2011-2015, Dr Yang Liao, Dr Wei Shi
License: GPL-3.0+
-Files: src/zpipe.c
-Copyright: Not copyrighted
-License: public-domain
-
Files: debian/*
Copyright: 2015 Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
License: GPL-3.0+
@@ -31,6 +27,3 @@ License: GPL-3.0+
.
On Debian systems, the complete text of the GNU General
Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
-
-License: public-domain
- Written by Mark Adler and put into the public domain.
diff --git a/debian/doc-base b/debian/doc-base
deleted file mode 100644
index 24013ba..0000000
--- a/debian/doc-base
+++ /dev/null
@@ -1,12 +0,0 @@
-Document: subread
-Title: Users Guide for subread aligner
-Author: Liao Y, Smyth GK, Shi W
-Abstract: The Subread/Rsubread packages comprise a suite of high-performance
- software programs for processing next-generation sequencing data. Included in
- these packages are Subread aligner, Subjunc aligner, Subindel long indel
- detection program, featureCounts read quantification program, exactSNP SNP
- calling program and other utility programs.
-Section: Science/Biology
-
-Format: pdf
-Files: /usr/share/doc/subread/SubreadUsersGuide.pdf
diff --git a/debian/patches/fix_repair_usage.patch b/debian/patches/fix_repair_usage.patch
new file mode 100644
index 0000000..ea033ef
--- /dev/null
+++ b/debian/patches/fix_repair_usage.patch
@@ -0,0 +1,13 @@
+Description: fix usage string, replace removeDup with repair
+Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+--- subread.orig/src/read-repair.c
++++ subread/src/read-repair.c
+@@ -16,7 +16,7 @@
+ SUBREADputs("");
+ SUBREADputs("Usage:");
+ SUBREADputs("");
+- SUBREADputs(" ./removeDup [options] -i <input_file> -o <output_file>\n");
++ SUBREADputs(" ./repair [options] -i <input_file> -o <output_file>\n");
+ SUBREADputs("");
+ SUBREADputs("Required arguments:");
+ SUBREADputs("");
diff --git a/debian/patches/fix_syntax.patch b/debian/patches/fix_syntax.patch
deleted file mode 100644
index 5297c76..0000000
--- a/debian/patches/fix_syntax.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-Description: spelling-error-in-binary subread-buildindex s/sucessfully/successfully/
-Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
---- subread.orig/src/index-builder.c
-+++ subread/src/index-builder.c
-@@ -958,7 +958,7 @@
- if(tmp_file_for_signal[0])
- {
- unlink(tmp_file_for_signal);
-- SUBREADprintf("\n\nReceived a terminal signal. The temporary file was removed. The index was NOT built sucessfully. Please DO NOT use the new index until they are rebuilt.\n\n");
-+ SUBREADprintf("\n\nReceived a terminal signal. The temporary file was removed. The index was NOT built successfully. Please DO NOT use the new index until they are rebuilt.\n\n");
- }
-
- exit(param);
diff --git a/debian/patches/series b/debian/patches/series
index 7f7ea57..fc3be28 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,3 @@
+syntax_err.patch
+fix_repair_usage.patch
arch_specific_flags.patch
diff --git a/debian/patches/syntax_err.patch b/debian/patches/syntax_err.patch
new file mode 100644
index 0000000..ca21aba
--- /dev/null
+++ b/debian/patches/syntax_err.patch
@@ -0,0 +1,13 @@
+Description: spelling-error-in-binary featureCounts s/requried/required/
+Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+--- subread.orig/src/readSummary.c
++++ subread/src/readSummary.c
+@@ -3368,7 +3368,7 @@
+ SUBREADputs(" --largestOverlap Assign reads to a meta-feature/feature that has the ");
+ SUBREADputs(" largest number of overlapping bases.");
+ SUBREADputs("");
+- SUBREADputs(" --minOverlap <int> Specify minimum number of overlapping bases requried ");
++ SUBREADputs(" --minOverlap <int> Specify minimum number of overlapping bases required ");
+ SUBREADputs(" between a read and a meta-feature/feature that the read ");
+ SUBREADputs(" is assigned to. 1 by default.");
+ SUBREADputs("");
diff --git a/debian/rules b/debian/rules
index 36a13e9..30e07a6 100755
--- a/debian/rules
+++ b/debian/rules
@@ -69,7 +69,7 @@ DNA-seq reads and RNA-seq reads (for the purpose of expression analysis)' \
$(HELP2MAN) --name='calculate the proportion of mapped reads/fragments' \
$(utildir)/propmapped | debian/filter.pl > $(mandir)/propmapped.1;
- for i in globalReassembly removeDup qualityScores subtools ; do \
+ for i in removeDup repair qualityScores ; do \
$(HELP2MAN) --name='a component of subread suite' $(utildir)/$$i | debian/filter.pl > $(mandir)/$$i.1; \
done
diff --git a/debian/subread.docs b/debian/subread.docs
index 05bd242..71dfd5b 100644
--- a/debian/subread.docs
+++ b/debian/subread.docs
@@ -1,2 +1 @@
README.txt
-doc/SubreadUsersGuide.pdf
diff --git a/debian/subread.install b/debian/subread.install
index 8a8d698..79922e1 100644
--- a/debian/subread.install
+++ b/debian/subread.install
@@ -5,9 +5,8 @@ bin/subjunc usr/bin
bin/subread-align usr/bin
bin/subread-buildindex usr/bin
bin/utilities/coverageCount usr/lib/subread
-bin/utilities/globalReassembly usr/lib/subread
bin/utilities/propmapped usr/lib/subread
bin/utilities/qualityScores usr/lib/subread
bin/utilities/removeDup usr/lib/subread
+bin/utilities/repair usr/lib/subread
bin/utilities/subread-fullscan usr/lib/subread
-bin/utilities/subtools usr/lib/subread
--
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