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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>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/t-coffee/-/commit/337171d82d9a63fb0ccd09b809ef743e72becd07">337171d8</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-04-20T21:02:31+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Extended path by Aaron M. Ucko
</pre>
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<h4>1 changed file:</h4>
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<li class="file-stats">
<a href="#94efd86d8f6c645a33c64529cc5f40591e3f8764">
debian/patches/bypass_legacy_blast.patch
</a>
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<h4>Changes:</h4>
<li id="94efd86d8f6c645a33c64529cc5f40591e3f8764">
<a href="https://salsa.debian.org/med-team/t-coffee/-/commit/337171d82d9a63fb0ccd09b809ef743e72becd07#94efd86d8f6c645a33c64529cc5f40591e3f8764"><strong>debian/patches/bypass_legacy_blast.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">@@ -5,6 +5,15 @@ Description: See origin</td>
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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">@@ -688,7 +688,7 @@</span> sub blast_msa</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> #&safe_system ("formatdb -i $db");</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if ($blast eq "blastp"){&safe_system ("blastall -i $infile -d $db -m7 -p blastp -o io");}</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ($blast eq "blastp"){&safe_system ("blastp -db $db -query $infile -out io -outfmt 5 -seg yes");}</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> elsif ($blast eq "blastn"){&safe_system ("blastn -query $infile -db $db -outfmt 5 -word_size 4 -out io");}</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> &set_blast_type ("io");</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"><span class="p">@@ -1183,7 +1183,7 @@</span> sub pg_is_installed</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> if ($r eq ""){$r=0;}</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> else {$r=1;}</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -14,6 +23,15 @@ Description: See origin</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> else {return $r;}</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="p">@@ -2597,7 +2597,7 @@</span> sub run_blast</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> &check_configuration ("blastall");</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> if ($method eq "blastp")</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> {</span>
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30
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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="blastall -d $db -i $infile -o $outfile -m7 -p blastp";</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;">+ $command="blastp -db $db -query $infile -out $outfile -outfmt 5 -seg yes";</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> }</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> &safe_system ($command);</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> }</span>
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17
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"><span class="p">@@ -2611,26 +2611,20 @@</span> sub run_blast</span>
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18
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> $cl_db=$db;</span>
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19
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> }</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -47,3 +65,21 @@ Description: See origin</td>
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47
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="diff"> }</span>
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48
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="diff"> print "$command\n";</span>
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49
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="diff"> &safe_system ($command);</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="p">@@ -2859,7 +2853,7 @@</span> sub seq2tblastx_lib</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> }</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> close (F);</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> &safe_system ("formatdb -i infile -p F");</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- &safe_system ("blastall -p tblastx -i infile -d infile -m 7 -S1>blast.output");</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ &safe_system ("tblastx -db infile -query infile -out blast.output -outfmt 5");</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> </span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> ncbi_tblastx_xml2lib_file ("outfile", file2string ("blast.output"));</span>
</pre>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> &set_temporary_dir ("unset",$mode, $method, "outfile",$outfile);</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="p">@@ -2890,7 +2884,7 @@</span> sub seq2tblastpx_lib</span>
</pre>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> close (F);</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> &safe_system("t_coffee -other_pg seq_reformat -in infile -output tblastx_db1 > tblastxdb");</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> &safe_system ("formatdb -i tblastxdb -p T");</span>
</pre>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- &safe_system ("blastall -p blastp -i tblastxdb -d tblastxdb -m7 >blast.output");</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ &safe_system ("blastp -db tblastxdb -query tblastxdb -out blast.output -outfmt 5");</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> ncbi_tblastpx_xml2lib_file ("outfile", file2string ("blast.output"), %s);</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> &set_temporary_dir ("unset",$mode, $method, "outfile",$outfile);</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> myexit ($EXIT_SUCCESS);</span></pre>
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