Mercurial > repos > iuc > sra_tools

diff sra_macros.xml @ 16:f61761f373ea draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit e00e33a3405201e8decbbb641ad0a8c3e16c8bef"
author iuc
date Wed, 29 Apr 2020 16:11:52 +0000
parents 54366e4d692a
children 37f09413ddbf
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line diff
--- a/sra_macros.xml	Fri Mar 20 16:36:52 2020 +0000
+++ b/sra_macros.xml	Wed Apr 29 16:11:52 2020 +0000
@@ -3,9 +3,14 @@
     <token name="@ACCESSIONS_FROM_FILE@">
         grep '^[[:space:]]*[E|S|D]RR[0-9]\{1,\}[[:space:]]*$'
     </token>
+    <token name="@COMPRESS@"><![CDATA[pigz -cqp \${GALAXY_SLOTS:-1}]]></token>
     <token name="@CONFIGURE_TIMEOUT@"><![CDATA[
         vdb-config --restore-defaults && vdb-config -s /http/timeout/read=10000 || true &&
     ]]></token>
+    <token name="@CONFIGURE_RETRY@"><![CDATA[
+        export SRA_PREFETCH_RETRIES=3 &&
+        export SRA_PREFETCH_ATTEMPT=1 &&
+    ]]></token>
     <token name="@SET_ACCESSIONS@"><![CDATA[
         #if $input.input_select=="file_list":
             for acc in `@ACCESSIONS_FROM_FILE@ '$input.file_list'` ;
@@ -18,6 +23,7 @@
     <macro name="requirements">
         <requirements>
             <requirement type="package" version="2.10.3">sra-tools</requirement>
+            <requirement type="package" version="2.3.4">pigz</requirement>
             <yield/>
         </requirements>
     </macro>