[med-svn] [Git][med-team/kissplice][master] 3 commits: Update dependencies
François Gindraud (@fgindraud)
gitlab at salsa.debian.org
Tue Apr 5 17:15:46 BST 2022
François Gindraud pushed to branch master at Debian Med / kissplice
Commits:
b802c7cf by Francois Gindraud at 2022-04-05T17:57:22+02:00
Update dependencies
Precise version for bcalm and cmake.
texlive-latex-base is insufficient, texlive-latex-recommended works fine
- - - - -
3523da9e by Francois Gindraud at 2022-04-05T18:04:20+02:00
Remove gcc10 patch
This patch fixed global variables not being declared as 'extern'.
This has been fixed upstream, so it is unneeded for the foreseeable
future.
- - - - -
25bb6b8b by Francois Gindraud at 2022-04-05T18:12:43+02:00
Replace redirection script with symlink to bcalm
Due to the internal structure of kissplice, usr/bin/kissplice expects
bcalm to be present at usr/lib/kissplice/bcalm along with other internal
binaries. This is done upstream to be able to ship a local bcalm binary
in the fallback case for less technical users, without colliding with
any preinstalled usr/bin/bcalm.
In the normal case usr/lib/kissplice/bcalm is a redirection bash script
as CMake cannot generate symlinks. Added mechanism in rules and links to
replace this script with a symlink to usr/bin/bcalm.
Previously usr/bin/kissplice was patched with directs paths to bcalm.
The new setup leaves usr/bin/kissplice untouched and should be less
likely to break if usr/bin/kissplice changes upstream.
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/links
- − debian/patches/gcc10.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,10 +1,16 @@
kissplice (2.6.0-1) UNRELEASED; urgency=medium
+ [ Andreas Tille ]
* Upstream moved to https://gitlab.inria.fr
* New upstream version
* Set upstream metadata fields: Repository, Repository-Browse.
* Build-Depends: texlive-latex-base
+ [ Francois Gindraud ]
+ * Update dependencies
+ * Remove gcc10 patch
+ * Replace redirection script with symlink to bcalm
+
-- Andreas Tille <tille at debian.org> Fri, 01 Apr 2022 11:44:54 +0200
kissplice (2.5.5+dfsg-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -6,12 +6,12 @@ Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-python,
- cmake,
+ cmake (>= 3.1),
python3-dev,
libpython3-stdlib,
zlib1g-dev,
- texlive-latex-base,
- bcalm <!nocheck>
+ texlive-latex-recommended,
+ bcalm (>= 2.2.2) <!nocheck>
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/kissplice
Vcs-Git: https://salsa.debian.org/med-team/kissplice.git
@@ -23,7 +23,7 @@ Architecture: any-amd64 any-arm64 any-mips64 any-mips64el any-ia64 any-ppc64 any
Depends: ${shlibs:Depends},
${misc:Depends},
${python3:Depends},
- bcalm
+ bcalm (>= 2.2.2)
Description: Detection of various kinds of polymorphisms in RNA-seq data
KisSplice is a piece of software that enables the analysis of RNA-seq data
with or without a reference genome. It is an exact local transcriptome
=====================================
debian/links
=====================================
@@ -1 +1,2 @@
usr/share/kissplice/kissplice.py usr/bin/kissplice
+usr/bin/bcalm usr/lib/kissplice/bcalm
=====================================
debian/patches/gcc10.patch deleted
=====================================
@@ -1,92 +0,0 @@
-Description: Fix for gcc-10 which implements -fno-common by default
-Author: Nilesh Patra <npatra974 at gmail.com>
-Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=972768
-Forwarded: no
-Last-Update: 2020-10-26
---- a/thirdparty/kissreads/include/commons.h
-+++ b/thirdparty/kissreads/include/commons.h
-@@ -49,28 +49,28 @@
- #include<zlib.h>
- typedef uint64_t kmer_type;
- //int artificial_overlap;
--char comp ['t'+1];
--char nuc [4];
--char standard_fasta;
--char silent;
--char quality;
--char only_print;
--int kmer_size;
--int size_seeds;
--int minimal_read_overlap;
--kmer_type mask_code_seed;
-+__attribute__((__common__)) char comp ['t'+1];
-+__attribute__((__common__)) char nuc [4];
-+__attribute__((__common__)) char standard_fasta;
-+__attribute__((__common__)) char silent;
-+__attribute__((__common__)) char quality;
-+__attribute__((__common__)) char only_print;
-+__attribute__((__common__)) int kmer_size;
-+__attribute__((__common__)) int size_seeds;
-+__attribute__((__common__)) int minimal_read_overlap;
-+__attribute__((__common__)) kmer_type mask_code_seed;
-
- #ifdef INPUT_FROM_KISSPLICE
--int kisspliceKmerSize;
--int min_overlap;
--int countingOption;
-+__attribute__((__common__)) int kisspliceKmerSize;
-+__attribute__((__common__)) int min_overlap;
-+__attribute__((__common__)) int countingOption;
- #endif
- int valid_character(const char c);
--int average_size_reads;
--int nb_event_sets;
--int number_of_read_sets;
--int size_before_reads_starting; // see fragment_info.h
--char * anykmer;
-+extern int average_size_reads;
-+extern int nb_event_sets;
-+__attribute__((__common__)) int number_of_read_sets;
-+extern int size_before_reads_starting; // see fragment_info.h
-+__attribute__((__common__)) char * anykmer;
- char ** sort_strings (char ** strings, int number);
- void * mymalloc(const int size);
- void * mycalloc(const int size, const int size_2);
-@@ -89,14 +89,14 @@
- int get_next_sequence_and_comments_for_fastq (gzFile file, char * sequence, char * comment, char * quality, char * line);
- int get_next_sequence_for_fastq (gzFile file, char * read, char * quality, char * readid, char * qualityid);
- int number_of_sequences_in_file(gzFile file, char * line);
--gzFile file;
-+__attribute__((__common__)) gzFile file;
-
--uint64_t sum_memory;
--uint64_t sum_memory_strdup;
-+__attribute__((__common__)) uint64_t sum_memory;
-+__attribute__((__common__)) uint64_t sum_memory_strdup;
-
--uint64_t mask_nbseed ;
--uint64_t mask_offset_seed;
--unsigned int nbits_nbseeds;
-+__attribute__((__common__)) uint64_t mask_nbseed ;
-+__attribute__((__common__)) uint64_t mask_offset_seed;
-+__attribute__((__common__)) unsigned int nbits_nbseeds;
-
- // macro to test if a variable is null (i.e., a malloc failed)
- #define test_alloc( variable) { if(variable == NULL){ fprintf(stderr,"cannot allocate memory for variable %s, exit\n",#variable); exit(1); }}
---- a/thirdparty/kissreads/include/fragment_index.h
-+++ b/thirdparty/kissreads/include/fragment_index.h
-@@ -49,10 +49,10 @@
- #include <couple.h>
-
-
--int number_of_starters;
--hash_t seeds; // hash table seed -> (fragment id, position)
--hash_t seeds_count;
--couple * seed_table;
-+__attribute__((__common__)) int number_of_starters;
-+__attribute__((__common__)) hash_t seeds; // hash table seed -> (fragment id, position)
-+__attribute__((__common__)) hash_t seeds_count;
-+__attribute__((__common__)) couple * seed_table;
-
- p_fragment_info * index_starters_from_input_file (const int k, int nb_events_per_set, const int nb_fragment_per_event, const char input_only_upper, const int index_stride); // read and store all starters presents in the pointed file. Index by seeds of length k all these starters.
-
=====================================
debian/patches/series
=====================================
@@ -1,2 +1 @@
tests-2to3.patch
-# gcc10.patch
=====================================
debian/rules
=====================================
@@ -23,6 +23,7 @@ override_dh_compress:
override_dh_install:
rm -rf debian/$(DEB_SOURCE)/usr/README.md debian/$(DEB_SOURCE)/build debian/$(DEB_SOURCE)/builds
+ rm -f debian/$(DEB_SOURCE)/usr/lib/kissplice/bcalm
mkdir -p debian/$(DEB_SOURCE)/usr/share/$(DEB_SOURCE)
mv debian/$(DEB_SOURCE)/usr/bin/kissplice debian/$(DEB_SOURCE)/usr/share/$(DEB_SOURCE)/kissplice.py
View it on GitLab: https://salsa.debian.org/med-team/kissplice/-/compare/77085cdba1508eaf4859b7874ad2b2bfdaaeae5a...25bb6b8b3a269173f4a6a491db5a753fd86a97a7
--
View it on GitLab: https://salsa.debian.org/med-team/kissplice/-/compare/77085cdba1508eaf4859b7874ad2b2bfdaaeae5a...25bb6b8b3a269173f4a6a491db5a753fd86a97a7
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