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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/t-coffee">Debian Med / t-coffee</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/t-coffee/-/commit/773699b71310396b4dc03d964cd117c84ee4ed22">773699b7</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-04-20T17:44:30+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Better way to deal with .pl extension in blast tools
</pre>
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#94efd86d8f6c645a33c64529cc5f40591e3f8764">
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+
debian/patches/bypass_legacy_blast.patch
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</a>
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<li class="file-stats">
<a href="#3b9f58f404a21e68bbabff8886ab6d069aaf3736">
debian/patches/probconsrna.patch
</a>
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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/t-coffee/-/commit/773699b71310396b4dc03d964cd117c84ee4ed22#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">t-coffee (13.41.0.28bdc39+dfsg-2) UNRELEASED; 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"> [ Aaron M. Ucko ]</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Better way to deal with .pl extension in blast tools</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 20 Apr 2020 17:43:49 +0200</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">t-coffee (13.41.0.28bdc39+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> [ Michael R. Crusoe ]</span>
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<li id="94efd86d8f6c645a33c64529cc5f40591e3f8764">
<a href="https://salsa.debian.org/med-team/t-coffee/-/commit/773699b71310396b4dc03d964cd117c84ee4ed22#94efd86d8f6c645a33c64529cc5f40591e3f8764"><strong>debian/patches/bypass_legacy_blast.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Date: Mon, 20 Apr 2020 10:52:40 -0400</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">From: "Aaron M. Ucko" <ucko@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Origin: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=956848#20</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Description: See origin</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/example/tc_generic_method.pl</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/example/tc_generic_method.pl</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -1183,7 +1183,7 @@</span> sub pg_is_installed</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> if ($r eq ""){$r=0;}</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> else {$r=1;}</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if ($r==0 && is_blast_package ($p)){return pg_is_installed ("legacy_blast.pl");}</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ($r==0 && is_blast_package ($p)){return pg_is_installed ("blastn");}</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> else {return $r;}</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"> }</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -2611,26 +2611,20 @@</span> sub run_blast</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> $cl_db=$db;</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ##</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> ## BLAST+ provide different binaries names and CLI options</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ## Use the 'legacy_blast.pl' to keep compatibility with old blast commands</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ##</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $path=`which legacy_blast.pl 2>/dev/null`; </span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $path=`dirname $path`; </span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- chomp($path);</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> if ($method eq "blastp"){</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- &check_configuration("legacy_blast.pl");</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $command="legacy_blast.pl blastpgp --path $path -d $cl_db -i $infile -o $outfile -m7 -j1";</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ &check_configuration("psiblast");</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $command="psiblast -db $cl_db -query $infile -num_iterations 1 -out $outfile -outfmt 5";</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> elsif ($method eq "psiblast")</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- &check_configuration("legacy_blast.pl");</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $command="legacy_blast.pl blastpgp --path $path -d $cl_db -i $infile -o $outfile -m7 -j5";</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ &check_configuration("psiblast");</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $command="psiblast -db $cl_db -query $infile -num_iterations 5 -out $outfile -outfmt 5";</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> elsif ($method eq "blastn")</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- &check_configuration("legacy_blast.pl");</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $command="legacy_blast.pl blastall --path $path -p blastn -d $cl_db -i $infile -o $outfile -m7 -W6";</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ &check_configuration("blastn");</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $command="blastn -task blastn -db $cl_db -query $infile -word_size 6 -out $outfile -outfmt 5";</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> print "$command\n";</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> &safe_system ($command);</span></pre>
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<a href="https://salsa.debian.org/med-team/t-coffee/-/commit/773699b71310396b4dc03d964cd117c84ee4ed22#3b9f58f404a21e68bbabff8886ab6d069aaf3736"><strong>debian/patches/probconsrna.patch</strong></a>
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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">@@ -3,8 +3,8 @@ Description: Debian-specific adjustment.</td>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Sat, 16 Aug 2014 00:19:42 +0200</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">--- <span class="idiff left right">T-COFFEE_distribution_Version_11.00.8cbe486.orig</span>/t_coffee_source/data_headers/programmes_define.h</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">T-COFFEE_distribution_Version_11.00.8cbe486</span>/t_coffee_source/data_headers/programmes_define.h</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- <span class="idiff left right">a</span>/t_coffee_source/data_headers/programmes_define.h</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;">+++ <span class="idiff left right">b</span>/t_coffee_source/data_headers/programmes_define.h</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="p">@@ -68,7 +68,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> #define POA_FILE1 "blosum80.mat"</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> </span>
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<a href="https://salsa.debian.org/med-team/t-coffee/-/commit/773699b71310396b4dc03d964cd117c84ee4ed22#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">probconsrna.patch</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">ncbi-blast++_has_dropped_pl_extension.patch</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"># ncbi-blast++_has_dropped_pl_extension.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">bypass_legacy_blast.patch</span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">use_debian_packaged_TMalign.patch</span>
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4
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">hardening.patch</span>
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5
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">set_proper_dir_permissions.patch</span>
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