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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/proteinortho">Debian Med / proteinortho</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/proteinortho/-/commit/eaeab34cc6a80d987e134c4e7d0ef52f8c213937">eaeab34c</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-10-29T01:28:59+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add patch to enable building with new diamond-aligner (Closes: #996407)
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<strong><a href="https://salsa.debian.org/med-team/proteinortho/-/commit/99f932913076ef73ec735b111ee17ee94a1ff9f5">99f93291</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-29T01:39:43+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Run cme
</pre>
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<strong><a href="https://salsa.debian.org/med-team/proteinortho/-/commit/a7e1aa44e800962eb21a707e9248b31da11db22d">a7e1aa44</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-29T01:39:43+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#f774cab8ae8af13f7e6955bc4f5e0c982018cd5d">
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+
debian/patches/ignore-warnings.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/876260e60c7887aed5e8fc557a07d6fc3ecfae82...a7e1aa44e800962eb21a707e9248b31da11db22d#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">proteinortho (6.0.31+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Add patch to enable building with</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> new diamond-aligner (Closes: #996407)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Run cme</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Fri, 29 Oct 2021 01:34:50 +0530</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">proteinortho (6.0.31+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * New upstream version 6.0.31+dfsg</span>
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<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/876260e60c7887aed5e8fc557a07d6fc3ecfae82...a7e1aa44e800962eb21a707e9248b31da11db22d#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: proteinortho</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org>, Nilesh Patra <nilesh@debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org>,</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Nilesh Patra <nilesh@debian.org></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +9,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> liblapack-dev | libatlas-base-dev | liblapack.so,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> diamond-aligner,</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> procps</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.1</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">6.0</span></span>
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12
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/proteinortho</span>
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13
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/proteinortho.git</span>
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14
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Homepage: https://gitlab.com/paulklemm_PHD/proteinortho</span>
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<li id="f774cab8ae8af13f7e6955bc4f5e0c982018cd5d">
<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/876260e60c7887aed5e8fc557a07d6fc3ecfae82...a7e1aa44e800962eb21a707e9248b31da11db22d#f774cab8ae8af13f7e6955bc4f5e0c982018cd5d"><strong>debian/patches/ignore-warnings.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Propagate --ignore-warnings to fix problem with new diamond, and also to make it work</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> like it was working in previous versions</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/996407</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Author: Nilesh Patra <nilesh@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Last-Update: 2021-10-29</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/proteinortho6.pl</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/proteinortho6.pl</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -2220,12 +2220,12 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> if ($verbose) {print STDERR "The database for '$file' is present and will be used\n";}</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> }else{</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> if ($verbose) {print STDERR "Building database for '$file'\t(".$gene_counter{$file}." sequences)\n";}</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- system("$makedb '$file' -d '$file.$blastmode' --quiet >\/dev\/null 2>\/dev\/null");</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ system("$makedb '$file' -d '$file.$blastmode' --quiet --ignore-warnings >\/dev\/null 2>\/dev\/null");</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> 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.$NC";}print "\n";</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> mkdir("$tmp_path/DB");</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> if($step==1){$oldkeep=$keep;$keep=1;}</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- system("$makedb '$file' -d '$tmp_path/DB/".basename($file).".$blastmode' --quiet >\/dev\/null 2>\/dev\/null");</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ system("$makedb '$file' -d '$tmp_path/DB/".basename($file).".$blastmode' --quiet --ignore-warnings >\/dev\/null 2>\/dev\/null");</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> system("ln -s '".abs_path($file)."' '$tmp_path/DB/".basename($file)."'");</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> if($?!=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 $blastmode\n- consider another blast algorithm (-p)\n- consider to submitting (mailing) this case to incoming+paulklemm-phd-proteinortho-7278443-issue-\@incoming.gitlab.com.");}</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="p">@@ -2472,7 +2472,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> #elsif ($blastmode eq "pblatp") {lock($threads_per_process); $command = $binpath."pblat -prot '$a' '$b' -threads=$threads_per_process -out=blast8 '$bla' >\/dev\/null 2>&1";}</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> #elsif ($blastmode eq "pblatn") {lock($threads_per_process); $command = $binpath."pblat '$a' '$b' -threads=$threads_per_process -out=blast8 '$bla' >\/dev\/null 2>&1";}</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> #elsif ($blastmode eq "pblatx") {lock($threads_per_process); $command = $binpath."pblat '$a' '$b' -t=dnax -q=dnax -threads=$threads_per_process -out=blast8 '$bla' >\/dev\/null 2>&1";}</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- elsif ($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 '$bla.tmp'" : "");}</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ elsif ($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 '$bla.tmp'" : "");}</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> elsif ($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' $printSTDERR";}</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> elsif ($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 $printSTDERR";}</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> elsif ($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";}</span></pre>
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<a href="https://salsa.debian.org/med-team/proteinortho/-/compare/876260e60c7887aed5e8fc557a07d6fc3ecfae82...a7e1aa44e800962eb21a707e9248b31da11db22d#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">deb_diamond</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">ignore-warnings.patch</span></pre>
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