diff --git a/tags/drap-v1.91.tgz b/tags/drap-v1.91.tgz index 24779df3b4cf84c5025d99368ead9993ef655984..1e692695f99e906e62dcb8199884dac8cbbe5fbd 100644 Binary files a/tags/drap-v1.91.tgz and b/tags/drap-v1.91.tgz differ diff --git a/tags/drap-v1.91/bin/write_jobs_files.pl b/tags/drap-v1.91/bin/write_jobs_files.pl index 843ce4293a84fb494ccf3e130ef87bad9e6c2428..c23c2bb75816f839c78bb79602ce8da4dd22f523 100755 --- a/tags/drap-v1.91/bin/write_jobs_files.pl +++ b/tags/drap-v1.91/bin/write_jobs_files.pl @@ -105,8 +105,8 @@ unless (step_complete($opt)) { unless (-f "$dir/.trim.over") { # need to known the k-mer size used for the normalization step unless ($opt->{no_norm}) { - ($min_length) = $opt->{norm} =~ /(:?-k|--ksize|--KMER_SIZE)\s+(\d+)/; - $min_length ||= $opt->{norm_source} eq 'trinity' ? 25 : 32; + ($min_length) = $opt->{norm} =~ /(?:-k|--ksize|--KMER_SIZE)\s+(\d+)/; + $min_length ||= $opt->{norm_src} eq 'trinity' ? 25 : 32; } $opt->{cmd} .= 'mkdir -p '.join(' ', map {"$dir/trim_".$_} (1 .. $opt->{pool}))."\n"; $opt->{cmd} .= sprintf("parallel --joblog %s/trim.log -j %d -N %d \\\n trim_galore --no_report_file %s-o %s/trim_'{#}' %s %s ';' \\\n", diff --git a/trunk/bin/write_jobs_files.pl b/trunk/bin/write_jobs_files.pl index b9596b18d1e0ab010386dd305bd0a0b1fb0eef60..9af2e2d813c66349305de97681ca424cdc60329d 100755 --- a/trunk/bin/write_jobs_files.pl +++ b/trunk/bin/write_jobs_files.pl @@ -105,8 +105,8 @@ unless (step_complete($opt)) { unless (-f "$dir/.trim.over") { # need to known the k-mer size used for the normalization step unless ($opt->{no_norm}) { - ($min_length) = $opt->{norm} =~ /(:?-k|--ksize|--KMER_SIZE)\s+(\d+)/; - $min_length ||= $opt->{norm_source} eq 'trinity' ? 25 : 32; + ($min_length) = $opt->{norm} =~ /(?:-k|--ksize|--KMER_SIZE)\s+(\d+)/; + $min_length ||= $opt->{norm_src} eq 'trinity' ? 25 : 32; } $opt->{cmd} .= 'mkdir -p '.join(' ', map {"$dir/trim_".$_} (1 .. $opt->{pool}))."\n"; $opt->{cmd} .= sprintf("parallel --joblog %s/trim.log -j %d -N %d \\\n trim_galore --no_report_file %s-o %s/trim_'{#}' %s %s ';' \\\n", diff --git a/trunk/doc/install.html b/trunk/doc/install.html index 9de0401e750d8831ad008f8db952ff5d88d9ef0b..052c7d0fdc5f7f431256b1614e624dbf41354ad5 100644 --- a/trunk/doc/install.html +++ b/trunk/doc/install.html @@ -305,8 +305,8 @@ </div> <h2>Download source</h2> <div> - <p>Download source from SVN<p> - <pre class="prettyprint">svn checkout svn://scm.mulcyber.toulouse.inra.fr/svnroot/drap/tags/drap-v1.91</pre> + <p>Download source from:<p> + <pre class="prettyprint">wget https://forgemia.inra.fr/cedric.cabau/drap/raw/master/tags/drap-v1.91.tgz</pre> </div> <h2>DockerFile</h2> <div> diff --git a/trunk/doc/lib/src/Dockerfile b/trunk/doc/lib/src/Dockerfile index 418784480ef34eeb773e4ac00a375a0e5a82297d..c1fabe5a829bf1c676998aeec9accbe849260bd9 100644 --- a/trunk/doc/lib/src/Dockerfile +++ b/trunk/doc/lib/src/Dockerfile @@ -168,7 +168,8 @@ RUN mkdir /usr/local/src/banks \ ## -- install DRAP -- ## RUN cd /usr/local/src \ - && svn checkout svn://scm.mulcyber.toulouse.inra.fr/svnroot/drap/tags/drap-v1.91 \ + && wget https://forgemia.inra.fr/cedric.cabau/drap/raw/master/tags/drap-v1.91.tgz \ + && tar -xzf drap-v1.91.tgz \ && cd drap-v1.91 \ && ln -s $PWD/runCheck /usr/local/bin/runCheck \ && ln -s $PWD/runDrap /usr/local/bin/runDrap \