[med-svn] [Git][med-team/subread][master] 6 commits: d/control: simplify architecture specification by using the provisions from...
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Thu Mar 7 10:35:13 GMT 2024
Michael R. Crusoe pushed to branch master at Debian Med / subread
Commits:
e91afdc6 by Michael R. Crusoe at 2024-03-07T08:57:54+01:00
d/control: simplify architecture specification by using the provisions from the architecture-properties package.
- - - - -
b199dacb by Michael R. Crusoe at 2024-03-07T09:07:00+01:00
d/rules: preserve original mm39_RefSeq_exon.txt.gz to enable building twice. Closes: #1049300
- - - - -
88121640 by Michael R. Crusoe at 2024-03-07T09:07:00+01:00
d/control: update description of subread-data to include the gene annotations for both the hh39 and mm39 genomes.
- - - - -
07ea3db5 by Michael R. Crusoe at 2024-03-07T09:18:08+01:00
d/patches/arch_specific_flags.patch: since -D_FILE_OFFSET_BITS=64 is set, use fopen() even on 32-bit systems. Thanks to blhc "E-pointer-trouble-at-implicit" for pointing this out.
- - - - -
a36b10d3 by Michael R. Crusoe at 2024-03-07T09:20:14+01:00
d/patches/cross.patch: deleted, as it was unused and incorporated into arch_specific_flags.patch by Alexandre Mestiashvili.
- - - - -
65393f2c by Michael R. Crusoe at 2024-03-07T11:34:26+01:00
d/upstream/metadata: add publications, bug info, changelog, link to user guide PDF.
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/patches/arch_specific_flags.patch
- − debian/patches/cross.patch
- debian/rules
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,22 @@
+subread (2.0.6+dfsg-3) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * d/control: simplify architecture specification by using the
+ provisions from the architecture-properties package.
+ * d/rules: preserve original mm39_RefSeq_exon.txt.gz to enable
+ building twice. Closes: #1049300
+ * d/control: update description of subread-data to include the gene
+ annotations for both the hh39 and mm39 genomes.
+ * d/patches/arch_specific_flags.patch: since -D_FILE_OFFSET_BITS=64 is
+ set, use fopen() even on 32-bit systems.
+ Thanks to blhc "E-pointer-trouble-at-implicit" for pointing this out.
+ * d/patches/cross.patch: deleted, as it was unused and incorporated
+ into arch_specific_flags.patch by Alexandre Mestiashvili.
+ * d/upstream/metadata: add publications, bug info, changelog, link to
+ user guide PDF.
+
+ -- Michael R. Crusoe <crusoe at debian.org> Thu, 07 Mar 2024 08:55:34 +0100
+
subread (2.0.6+dfsg-2) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -6,6 +6,7 @@ Section: science
Priority: optional
Build-Depends: bc <!nocheck>,
debhelper-compat (= 13),
+ architecture-is-little-endian,
python3 <!nocheck>,
zlib1g-dev
Standards-Version: 4.6.2
@@ -15,7 +16,7 @@ Homepage: http://sourceforge.net/projects/subread/
Rules-Requires-Root: no
Package: subread
-Architecture: amd64 arm64 armel armhf i386 kfreebsd-amd64 kfreebsd-i386 ppc64el riscv64 loong64
+Architecture: any
Depends: ${misc:Depends},
${shlibs:Depends}
Description: toolkit for processing next-gen sequencing data
@@ -32,7 +33,7 @@ Multi-Arch: foreign
Description: data files for subread package
This package provides data files from the original tarball:
- annotation: Directory including NCBI RefSeq gene annotations for
- genomes 'hg19', 'mm10' and 'mm9'. Each row is an exon.
+ genomes 'hg19', 'hg39', 'mm9', 'mm10', and 'mm39'. Each row is an exon.
Entrez gene identifiers and chromosomal coordinates are provided for
each exon.
- test: Directory including test data and scripts.
=====================================
debian/patches/arch_specific_flags.patch
=====================================
@@ -134,3 +134,17 @@ From: Alex Mestiashvili <mestia at debian.org>
- $(CC) -o $@ -c $(subst .o,.c,$@)
-
+ $(CC) ${CFLAGS} ${CPPFLAGS} -o $@ -c $(subst .o,.c,$@)
+--- subread.orig/src/input-files.c
++++ subread/src/input-files.c
+@@ -48,11 +48,7 @@
+ #ifdef __MINGW32__
+ return fopen64(fname, mode);
+ #else
+-#if defined(__LP64__) || defined(_LP64) || defined(MACOS)
+ return fopen(fname, mode);
+-#else
+- return fopen64(fname, mode);
+-#endif
+ #endif
+
+ }
=====================================
debian/patches/cross.patch deleted
=====================================
@@ -1,122 +0,0 @@
-Description: Make build cross buildable -- fix compilation flags
-Author: Nilesh Patra <nilesh at debian.org>
-Last-Update: 2021-03-11
---- a/src/Makefile.Linux
-+++ b/src/Makefile.Linux
-@@ -1,7 +1,5 @@
- #MACOS = -D MACOS
-
--
--CC_EXEC = gcc
- OPT_LEVEL = 3
-
- include makefile.version
-@@ -9,7 +7,7 @@
-
- CCFLAGS += -O${OPT_LEVEL} -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\"${SUBREAD_VERSION}\" -D_FILE_OFFSET_BITS=64 ${WARNING_LEVEL}
- LDFLAGS += ${STATIC_MAKE} -pthread -lz -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm
--CC = ${CC_EXEC} ${CCFLAGS} ${CFLAGS} ${CPPFLAGS} -fmessage-length=0 -ggdb
-+CFLAGS += ${CCFLAGS} -fmessage-length=0 -ggdb
-
-
- ALL_LIBS= core core-junction core-indel sambam-file sublog gene-algorithms hashtable input-files sorted-hashtable gene-value-index exon-algorithms HelperFunctions interval_merge long-hashtable core-bigtable seek-zlib input-blc
-@@ -38,55 +36,55 @@
- cd longread-one && $(MAKE)
-
- genRandomReads: gen_rand_reads.c ${ALL_OBJECTS}
-- ${CC} -o genRandomReads gen_rand_reads.c ${ALL_OBJECTS} ${LDFLAGS}
-+ ${CC} ${CFLAGS} ${CPPFLAGS} -o genRandomReads gen_rand_reads.c ${ALL_OBJECTS} ${LDFLAGS}
-
- flattenGTF: flattenAnnotations.c ${ALL_OBJECTS}
-- ${CC} -o flattenGTF flattenAnnotations.c ${ALL_OBJECTS} ${LDFLAGS}
-+ ${CC} ${CFLAGS} ${CPPFLAGS} -o flattenGTF flattenAnnotations.c ${ALL_OBJECTS} ${LDFLAGS}
-
- detectionCall: detection-calls.c ${ALL_OBJECTS}
-- ${CC} -o detectionCall detection-calls.c ${ALL_OBJECTS} ${LDFLAGS}
-+ ${CC} ${CFLAGS} ${CPPFLAGS} -o detectionCall detection-calls.c ${ALL_OBJECTS} ${LDFLAGS}
-
- repair: read-repair.c ${ALL_OBJECTS}
-- ${CC} -o repair read-repair.c ${ALL_OBJECTS} ${LDFLAGS}
-+ ${CC} ${CFLAGS} ${CPPFLAGS} -o repair read-repair.c ${ALL_OBJECTS} ${LDFLAGS}
-
- txUnique: tx-unique.c tx-unique.h ${ALL_OBJECTS}
-- ${CC} -o txUnique tx-unique.c ${ALL_OBJECTS} ${LDFLAGS}
-+ ${CC} ${CFLAGS} ${CPPFLAGS} -o txUnique tx-unique.c ${ALL_OBJECTS} ${LDFLAGS}
-
- globalReassembly: global-reassembly.c ${ALL_OBJECTS}
-- ${CC} -o globalReassembly global-reassembly.c ${ALL_OBJECTS} ${LDFLAGS}
-+ ${CC} ${CFLAGS} ${CPPFLAGS} -o globalReassembly global-reassembly.c ${ALL_OBJECTS} ${LDFLAGS}
-
- propmapped: propmapped.c ${ALL_OBJECTS}
-- ${CC} -o propmapped propmapped.c ${ALL_OBJECTS} ${LDFLAGS}
-+ ${CC} ${CFLAGS} ${CPPFLAGS} -o propmapped propmapped.c ${ALL_OBJECTS} ${LDFLAGS}
-
- exactSNP: SNPCalling.c SNPCalling.h ${ALL_OBJECTS}
-- ${CC} -o exactSNP SNPCalling.c ${ALL_OBJECTS} ${LDFLAGS}
-+ ${CC} ${CFLAGS} ${CPPFLAGS} -o exactSNP SNPCalling.c ${ALL_OBJECTS} ${LDFLAGS}
-
- subread-buildindex: index-builder.c subread.h ${ALL_OBJECTS}
-- ${CC} -o subread-buildindex index-builder.c ${ALL_OBJECTS} ${LDFLAGS}
-+ ${CC} ${CFLAGS} ${CPPFLAGS} -o subread-buildindex index-builder.c ${ALL_OBJECTS} ${LDFLAGS}
-
- removeDup: removeDupReads.c removeDupReads.h subread.h ${ALL_OBJECTS}
-- ${CC} -o removeDup removeDupReads.c ${ALL_OBJECTS} ${LDFLAGS}
-+ ${CC} ${CFLAGS} ${CPPFLAGS} -o removeDup removeDupReads.c ${ALL_OBJECTS} ${LDFLAGS}
-
- subindel: SUBindel.c core.h subread.h ${ALL_OBJECTS}
-- ${CC} -o subindel SUBindel.c ${ALL_OBJECTS} ${LDFLAGS}
-+ ${CC} ${CFLAGS} ${CPPFLAGS} -o subindel SUBindel.c ${ALL_OBJECTS} ${LDFLAGS}
-
- featureCounts: readSummary.c subread.h ${ALL_OBJECTS}
-- ${CC} -o featureCounts readSummary.c ${ALL_OBJECTS} ${LDFLAGS}
-+ ${CC} ${CFLAGS} ${CPPFLAGS} -o featureCounts readSummary.c ${ALL_OBJECTS} ${LDFLAGS}
-
- subread-align: core-interface-aligner.c ${ALL_OBJECTS}
-- ${CC} -o subread-align core-interface-aligner.c ${ALL_OBJECTS} ${LDFLAGS}
-+ ${CC} ${CFLAGS} ${CPPFLAGS} -o subread-align core-interface-aligner.c ${ALL_OBJECTS} ${LDFLAGS}
-
- subjunc: core-interface-subjunc.c ${ALL_OBJECTS}
-- ${CC} -o subjunc core-interface-subjunc.c ${ALL_OBJECTS} ${LDFLAGS}
-+ ${CC} ${CFLAGS} ${CPPFLAGS} -o subjunc core-interface-subjunc.c ${ALL_OBJECTS} ${LDFLAGS}
-
- subtools: subtools.c ${ALL_OBJECTS}
-- ${CC} -o subtools subtools.c ${ALL_OBJECTS} ${LDFLAGS}
-+ ${CC} ${CFLAGS} ${CPPFLAGS} -o subtools subtools.c ${ALL_OBJECTS} ${LDFLAGS}
-
- qualityScores: qualityScores.c ${ALL_OBJECTS}
-- ${CC} -o qualityScores qualityScores.c ${ALL_OBJECTS} ${LDFLAGS}
-+ ${CC} ${CFLAGS} ${CPPFLAGS} -o qualityScores qualityScores.c ${ALL_OBJECTS} ${LDFLAGS}
-
- subread-fullscan: fullscan.c ${ALL_OBJECTS}
-- ${CC} -o subread-fullscan fullscan.c ${ALL_OBJECTS} ${LDFLAGS}
-+ ${CC} ${CFLAGS} ${CPPFLAGS} -o subread-fullscan fullscan.c ${ALL_OBJECTS} ${LDFLAGS}
-
- clean:
- rm -f core featureCounts exactSNP removeDup subread-buildindex ${ALL_OBJECTS}
---- a/src/longread-one/Makefile
-+++ b/src/longread-one/Makefile
-@@ -1,4 +1,3 @@
--CC_EXEC = gcc
- OPT_LEVEL = 3
-
- include ../makefile.version
-@@ -6,7 +5,7 @@
-
- CCFLAGS += -O${OPT_LEVEL} -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" ${WARNING_LEVEL} ${MINGW32}
- LDFLAGS += -lpthread -lz -lm -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST
--CC = ${CC_EXEC} ${CFLAGS} ${CPPFLAGS} ${CCFLAGS} -fmessage-length=0 -ggdb
-+CFLAGS += ${CCFLAGS} -fmessage-length=0 -ggdb
-
- ALL_LIBS=LRMsorted-hashtable LRMbase-index LRMchro-event LRMhelper LRMseek-zlib LRMfile-io LRMhashtable
- ALL_OBJECTS=$(addsuffix .o, ${ALL_LIBS})
-@@ -20,8 +19,8 @@
- rm -f *.o LRM
-
- LRM: longread-mapping.c ${ALL_OBJECTS}
-- ${CC} -o LRM longread-mapping.c ${ALL_OBJECTS} ${LDFLAGS}
-+ ${CC} $(CFLAGS) $(CPPFLAGS) -o LRM longread-mapping.c ${ALL_OBJECTS} ${LDFLAGS}
-
- $(ALL_OBJECTS): $(ALL_C) $(ALL_H)
-- $(CC) -o $@ -c $(subst .o,.c,$@)
-+ $(CC) $(CFLAGS) $(CPPFLAGS) -o $@ -c $(subst .o,.c,$@)
-
=====================================
debian/rules
=====================================
@@ -35,8 +35,10 @@ endif
override_dh_auto_install:
#fix for gzip-file-is-not-multi-arch-same-safe
+ cp annotation/mm39_RefSeq_exon.txt.gz debian/mm39_RefSeq_exon.txt.gz.orig
find $(CURDIR) -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "$${name%.*}"' \;
dh_auto_install
+ mv debian/mm39_RefSeq_exon.txt.gz.orig annotation/mm39_RefSeq_exon.txt.gz
override_dh_installexamples-indep:
tar --sort=name \
=====================================
debian/upstream/metadata
=====================================
@@ -1,4 +1,56 @@
+Bug-Database: https://sourceforge.net/p/subread/bugs/
+Bug-Submit: https://support.bioconductor.org/
+Changelog: https://subread.sourceforge.net/
+Documentation: https://subread.sourceforge.net/SubreadUsersGuide.pdf
Archive: SourceForge
+Reference:
+- # If you use Rsubread, you can cite:
+ Author: Yang Lian and Gordon K. Smyth and Wei Shi
+ Title: The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads
+ Journal: Nucleic Acids Research
+ Year: 2019
+ Volume: 47
+ Number: 8
+ Pages: e47-e47
+ DOI: 10.1093/nar/gkz114
+ PMID: 30783653
+ URL: https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/30783653/
+- # If you use Subread or Subjunc aligners, you can cite:
+ Author: Yang Lian and Gordon K. Smyth and Wei Shi
+ Title: |
+ The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote
+ Journal: Nucleic Acids Research
+ Year: 2013
+ Volume: 41
+ Number: 10
+ Pages: e108–e108
+ DOI: 10.1093/nar/gkt214
+ PMID: 23558742
+ URL: https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23558742/
+ Publisher: Oxford University Press (OUP)
+ Type: article
+- # If you use featureCounts, you can cite:
+ Author: Yang Lian and Gordon K. Smyth and Wei Shi
+ Title: |
+ featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
+ Journal: Bioinformatics
+ Year: 2014
+ Volume: 30
+ Number: 7
+ Pages: 923–930
+ DOI: 10.1093/bioinformatics/btt656
+ PMID: 24227677
+ URL: https://academic.oup.com/bioinformatics/article/30/7/923/232889?
+- # If you use Rsubread inbuilt annotations, you can cite:
+ Author: David Chisanga and Yang Liao and Wei Shi}
+ Title: Impact of gene annotation choice on the quantification of RNA-seq data
+ Journal: BMC Bioinformatics
+ Year: 2022
+ Volume: 23
+ Number: 1
+ DOI: 10.1186/s12859-022-04644-8
+ PMID: 35354358
+ URL: https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/35354358/
Registry:
- Name: OMICtools
Entry: OMICS_01255
View it on GitLab: https://salsa.debian.org/med-team/subread/-/compare/3ec4417e8afbc3d48583bbb83dd33662d1dcbf59...65393f2cbdfde97bdd523a399a47e4b7bc4cfe37
--
View it on GitLab: https://salsa.debian.org/med-team/subread/-/compare/3ec4417e8afbc3d48583bbb83dd33662d1dcbf59...65393f2cbdfde97bdd523a399a47e4b7bc4cfe37
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