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 <[email protected]> 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 <[email protected]> -Uploaders: Andreas Tille <[email protected]>, Nilesh Patra <[email protected]> +Uploaders: Andreas Tille <[email protected]>, + Nilesh Patra <[email protected]> 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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