[med-svn] [Git][med-team/proteinortho][master] 3 commits: Add patch to enable building with new diamond-aligner (Closes: #996407)
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Thu Oct 28 21:12:43 BST 2021
Nilesh Patra pushed to branch master at Debian Med / proteinortho
Commits:
eaeab34c by Nilesh Patra at 2021-10-29T01:28:59+05:30
Add patch to enable building with new diamond-aligner (Closes: #996407)
- - - - -
99f93291 by Nilesh Patra at 2021-10-29T01:39:43+05:30
Run cme
- - - - -
a7e1aa44 by Nilesh Patra at 2021-10-29T01:39:43+05:30
Upload to unstable
- - - - -
4 changed files:
- debian/changelog
- debian/control
- + debian/patches/ignore-warnings.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+proteinortho (6.0.31+dfsg-2) unstable; urgency=medium
+
+ * Add patch to enable building with
+ new diamond-aligner (Closes: #996407)
+ * Run cme
+
+ -- Nilesh Patra <nilesh at debian.org> Fri, 29 Oct 2021 01:34:50 +0530
+
proteinortho (6.0.31+dfsg-1) unstable; urgency=medium
* New upstream version 6.0.31+dfsg
=====================================
debian/control
=====================================
@@ -1,6 +1,7 @@
Source: proteinortho
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>, Nilesh Patra <nilesh at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+ Nilesh Patra <nilesh at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
@@ -8,7 +9,7 @@ Build-Depends: debhelper-compat (= 13),
liblapack-dev | libatlas-base-dev | liblapack.so,
diamond-aligner,
procps
-Standards-Version: 4.5.1
+Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/proteinortho
Vcs-Git: https://salsa.debian.org/med-team/proteinortho.git
Homepage: https://gitlab.com/paulklemm_PHD/proteinortho
=====================================
debian/patches/ignore-warnings.patch
=====================================
@@ -0,0 +1,31 @@
+Description: Propagate --ignore-warnings to fix problem with new diamond, and also to make it work
+ like it was working in previous versions
+Bug-Debian: https://bugs.debian.org/996407
+Author: Nilesh Patra <nilesh at debian.org>
+Last-Update: 2021-10-29
+--- a/proteinortho6.pl
++++ b/proteinortho6.pl
+@@ -2220,12 +2220,12 @@
+ if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}
+ }else{
+ if ($verbose) {print STDERR "Building database for '$file'\t(".$gene_counter{$file}." sequences)\n";}
+- system("$makedb '$file' -d '$file.$blastmode' --quiet >\/dev\/null 2>\/dev\/null");
++ system("$makedb '$file' -d '$file.$blastmode' --quiet --ignore-warnings >\/dev\/null 2>\/dev\/null");
+ if ($? != 0) {print STDERR ("$ORANGE\n[WARNING]$NC ".$blastmode." failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in $tmp_path (-tmp)."); if($step==1){print STDERR "$ORANGE Please ensure that you use -tmp=$tmp_path -keep (and use the same -project= name) for future analysis.$NC";}print "\n";
+
+ mkdir("$tmp_path/DB");
+ if($step==1){$oldkeep=$keep;$keep=1;}
+- system("$makedb '$file' -d '$tmp_path/DB/".basename($file).".$blastmode' --quiet >\/dev\/null 2>\/dev\/null");
++ system("$makedb '$file' -d '$tmp_path/DB/".basename($file).".$blastmode' --quiet --ignore-warnings >\/dev\/null 2>\/dev\/null");
+ system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");
+
+ if($?!=0){ $keep=$oldkeep; &Error("The database generation failed once again, please retry with 'sudo' or move the fasta files to a directory with write permissions. If this fails too, then there is something wrong with the fasta files or the version of $blastmode cannot handle the database generation. So please try one of the following:\n- update $blastmode\n- consider another blast algorithm (-p)\n- consider to submitting (mailing) this case to incoming+paulklemm-phd-proteinortho-7278443-issue-\@incoming.gitlab.com.");}
+@@ -2472,7 +2472,7 @@
+ #elsif ($blastmode eq "pblatp") {lock($threads_per_process); $command = $binpath."pblat -prot '$a' '$b' -threads=$threads_per_process -out=blast8 '$bla' >\/dev\/null 2>&1";}
+ #elsif ($blastmode eq "pblatn") {lock($threads_per_process); $command = $binpath."pblat '$a' '$b' -threads=$threads_per_process -out=blast8 '$bla' >\/dev\/null 2>&1";}
+ #elsif ($blastmode eq "pblatx") {lock($threads_per_process); $command = $binpath."pblat '$a' '$b' -t=dnax -q=dnax -threads=$threads_per_process -out=blast8 '$bla' >\/dev\/null 2>&1";}
+- elsif ($blastmode eq "diamond" ) {lock($threads_per_process); $command = $binpath."diamond blastp --threads $threads_per_process --db '$a.$blastmode' --query '$b' -e $evalue --outfmt 6 --quiet $blastOptions $blastOptions_diamond $printSTDERR ".($keep ? " | tee '$bla.tmp'" : "");}
++ elsif ($blastmode eq "diamond" ) {lock($threads_per_process); $command = $binpath."diamond blastp --threads $threads_per_process --db '$a.$blastmode' --query '$b' -e $evalue --outfmt 6 --quiet --ignore-warnings $blastOptions $blastOptions_diamond $printSTDERR ".($keep ? " | tee '$bla.tmp'" : "");}
+ elsif ($blastmode eq "topaz" ) {lock($threads_per_process); $command = $binpath."topaz search -T $threads_per_process -p '$a.$blastmode' -f '$b' -E $evalue --blasttab $blastOptions >'$bla.tmp' $printSTDERR";}
+ elsif ($blastmode eq "ublast") {lock($threads_per_process); $command = $binpath."usearch -ublast '$b' -db '$a.$blastmode' -threads $threads_per_process -evalue $evalue -blast6out '$bla.tmp' $blastOptions >\/dev\/null $printSTDERR";}
+ elsif ($blastmode eq "usearch") {lock($threads_per_process); $command = $binpath."usearch -usearch_local '$b' -db '$a.$blastmode' -threads $threads_per_process -evalue $evalue -id 0 -blast6out '$bla.tmp' $blastOptions >\/dev\/null $printSTDERR";}
=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
deb_diamond
+ignore-warnings.patch
View it on GitLab: https://salsa.debian.org/med-team/proteinortho/-/compare/876260e60c7887aed5e8fc557a07d6fc3ecfae82...a7e1aa44e800962eb21a707e9248b31da11db22d
--
View it on GitLab: https://salsa.debian.org/med-team/proteinortho/-/compare/876260e60c7887aed5e8fc557a07d6fc3ecfae82...a7e1aa44e800962eb21a707e9248b31da11db22d
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