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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/snpeff">Debian Med / snpeff</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/snpeff/-/commit/6d58a59db0033e540479082abb5fbcafc3fdaf54">6d58a59d</a></strong>
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<span>by Pierre Gruet</span>
<i>at 2021-02-21T22:49:36+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Putting config file and downloaded data in a dot directory by default
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<h4>5 changed files:</h4>
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<a href="#f168b81935360ddcf2dd0f2d4b98b8603829060f">
debian/README.Debian
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#fc93cb17d5957919628da13ce0195e57878a1c59">
debian/manpages/snpEff.1
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<a href="#94bfc9b7b2edebd4dc49a7edd537fcb53d71efa6">
debian/patches/update_launching_script_for_Debian.patch
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debian/patches/update_launching_script_and_config_file_for_Debian.patch
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<h4>Changes:</h4>
<li id="f168b81935360ddcf2dd0f2d4b98b8603829060f">
<a href="https://salsa.debian.org/med-team/snpeff/-/commit/6d58a59db0033e540479082abb5fbcafc3fdaf54#f168b81935360ddcf2dd0f2d4b98b8603829060f"><strong>debian/README.Debian</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">When getting SnpEff from the upstream source repository, the configuration file snpEff.config usually sits next to the jar; this is not the case for the Debian packaging, because the jar is in /usr/share/java.</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">So I am shipping a default /etc/snpEff.config file and it will be copied into ~/.snpEff.config, which will be used, if the latter does not exist and if no other config file is given in the command line invocation.</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">When getting SnpEff from the upstream source repository, the configuration file</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">snpEff.config usually sits next to the jar; this is not the case for the Debian</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">packaging, because the jar is in /usr/share/java. So I am shipping a default</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">/etc/snpEff.config file and it will be copied into ~/.snpEff/snpEff.config,</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">which will be used, if the latter does not exist and if no other config file is</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">given in the command line invocation.</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="LC4" class="line" lang="plaintext"> -- Pierre Gruet <pgtdebian@free.fr> Fri, 19 Feb 2021 09:22:13 +0100</span></pre>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Moreover, by default data downloaded from the Internet by snpEff will be put</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">into ~/.snpEff/data. The users can change this by editing their per-user config</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">file ~/.snpEff/snpEff.config or by providing another config file on the command</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">line.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> -- Pierre Gruet <pgtdebian@free.fr> Sun, 21 Feb 2021 15:45:10 +0100</span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/snpeff/-/commit/6d58a59db0033e540479082abb5fbcafc3fdaf54#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</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">@@ -4,8 +4,11 @@ snpeff (4.3t+dfsg-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> TODO:</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> - Ensure upstream provides files with proper copyrighting and licensing.</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> - fill in debian/copyright, maybe remove the html/ folder.</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> - check my patch replacing akka with java.util.concurrent.</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> - snpsift is to package elsewhere on its own.</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> - add autopkgtest</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> - add autopkgtest if possible, as many many tasks need downloading data</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> from the Internet before.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> - Find out where the build date is recorded and stored (it is then</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> outputted as shown, for instance, in the example from the website) to</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> allow for build reproducibility.</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> -- Pierre Gruet <pgtdebian@free.fr> Fri, 19 Feb 2021 09:47:24 +0100</span></pre>
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<a href="https://salsa.debian.org/med-team/snpeff/-/commit/6d58a59db0033e540479082abb5fbcafc3fdaf54#fc93cb17d5957919628da13ce0195e57878a1c59"><strong>debian/manpages/snpEff.1</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">@@ -59,7 +59,7 @@ Create a translocations report (from VCF file).</td>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext">.SS "Generic options"</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext">\fB\-c\fR , \fB\-config\fR</span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">Specify config file</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">Specify config file<span class="idiff left right">. Default: ~/.snpEff/snpEff.config</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext">\fB\-configOption\fR name=value</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext">Override a config file option</span>
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<a href="https://salsa.debian.org/med-team/snpeff/-/commit/6d58a59db0033e540479082abb5fbcafc3fdaf54#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -4,4 +4,4 @@ adapting_to_htsjdk.patch</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">adding_scala_in_pom.patch</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">fix_tests.patch</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">alter_pom_for_debian_packaging.patch</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">update_launching_script_for_Debian.patch</span></pre>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">update_launching_script_<span class="idiff left right">and_config_file_</span>for_Debian.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/snpeff/-/commit/6d58a59db0033e540479082abb5fbcafc3fdaf54#94bfc9b7b2edebd4dc49a7edd537fcb53d71efa6"><strong>debian/patches/update_launching_script_for_Debian.patch</strong>
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<strong>debian/patches/update_launching_script_and_config_file_for_Debian.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: Alter the launching script <span class="idiff left right">fora Debian installation</span></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Alter the launching script <span class="idiff left right">and the config filefor a Debian install</span></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"> - Simplify the paths to account for a Debian installation.</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"> - Use the default /etc/snpEff.config file as configuration file if no file was</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> given in the command line: it will be copied into ~/.snpEff.config, which will</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> be used as the config file is no other is given on the command line.</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> - Correct bashisms.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> given in the command line: it will be copied into ~/.snpEff/snpEff.config,</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> which will be used as the configuration file is no other is given on the</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> command line.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> - By default, put data in ~/.snpEff/data.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> - Correct bashisms in the launching script.</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian@free.fr></span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="p">Last-Update: 2021-02-<span class="idiff left right">19</span></span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">Last-Update: 2021-02-<span class="idiff left right">21</span></span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff">--- a/scripts/snpEff</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/snpEff</span></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">@@ -31,7 +33,7 @@ Last-Update: 2021-02-19</td>
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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"> default_jvm_mem_opts="-Xms1g -Xmx4g"</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"> jvm_mem_opts=""</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="p">@@ -39,12 +33,<span class="idiff left right">16</span> @@</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="p">@@ -39,12 +33,<span class="idiff left right">20</span> @@</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> esac</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"> done</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"> </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">@@ -42,13 +44,28 @@ Last-Update: 2021-02-19</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if [[ "$pass_args" != "" && ! "$pass_args" =~ "-c " ]]; then</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pass_args="$pass_args -c ${jardir}/snpEff.config"</span></span>
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if [ "$pass_args" != "" ] && ! echo "$pass_args" | grep "\-c " ; then</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if [ ! -<span class="idiff left right">e ~/.snpEff.config</span> ]; then</span></span>
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46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <span class="idiff left right">cp /etc/snpEff.config ~/.snpEff.config</span></span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if [ ! -<span class="idiff left right">d ~/.snpEff</span> ]; then</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <span class="idiff left right">mkdir ~/.snpEff</span></span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fi</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pass_args="$pass_args -c $HOME/.snpEff.config"</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if [ -d ~/.snpEff -a ! -e ~/.snpEff/snpEff.config ]; then</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cp /etc/snpEff.config ~/.snpEff/snpEff.config</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fi</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pass_args="$pass_args -c $HOME/.snpEff/snpEff.config"</span></span>
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> fi</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"> </span>
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52
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-exec $java $jvm_mem_opts $jvm_prop_opts -jar ${jardir}/snpEff.jar $pass_args</span></span>
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53
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+exec java $jvm_mem_opts $jvm_prop_opts -jar ${jardir}/snpeff.jar $pass_args</span></span>
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> exit</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/snpEff.config</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/snpEff.config</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="p">@@ -14,7 +14,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> # Also, a non-absolute path will be relative to config's file dir</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> # </span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> #---</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-data.dir = ./data/</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+data.dir = ~/.snpEff/data/</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> #---</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> # Database repository: A URL to the server where you can download databases (command: 'snpEff download dbName')</span></pre>
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