Mercurial > repos > iuc > sra_tools

diff sra_macros.xml @ 18:7068f48d0ef9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d22c001db39b52ebaa54837bebe2765c17b5c876"
author iuc
date Mon, 08 Jun 2020 05:49:21 -0400
parents c441583adae5
children 248f85ff0733
line wrap: on
line diff
--- a/sra_macros.xml	Wed Apr 29 12:12:23 2020 -0400
+++ b/sra_macros.xml	Mon Jun 08 05:49:21 2020 -0400
@@ -1,16 +1,22 @@
 <macros>
-    <token name="@VERSION@">2.10.4</token>
+    <token name="@VERSION@">2.10.7</token>
     <token name="@ACCESSIONS_FROM_FILE@">
         grep '^[[:space:]]*[E|S|D]RR[0-9]\{1,\}[[:space:]]*$'
     </token>
     <token name="@COMPRESS@"><![CDATA[pigz -cqp \${GALAXY_SLOTS:-1}]]></token>
-    <token name="@CONFIGURE_TIMEOUT@"><![CDATA[
-        vdb-config --restore-defaults && vdb-config -s /http/timeout/read=10000 || true &&
-    ]]></token>
     <token name="@CONFIGURE_RETRY@"><![CDATA[
         export SRA_PREFETCH_RETRIES=3 &&
         export SRA_PREFETCH_ATTEMPT=1 &&
     ]]></token>
+    <token name="@COPY_CONFIGFILE@"><![CDATA[
+    mkdir -p ~/.ncbi &&
+    cp '$user_settings_mkfg' ~/.ncbi/user-settings.mkfg &&
+    vdb-config -s "/repository/user/main/public/root=\$PWD" &&
+    vdb-config -s "/repository/user/ad/public/root=\$PWD" &&
+    vdb-config -s "/repository/user/default-path=\$PWD" &&
+    vdb-config -s "/repository/user/main/public/root=\$PWD" &&
+    vdb-config -s /http/timeout/read=10000 &&
+    ]]></token>
     <token name="@SET_ACCESSIONS@"><![CDATA[
         #if $input.input_select=="file_list":
             for acc in `@ACCESSIONS_FROM_FILE@ '$input.file_list'` ;
@@ -22,11 +28,21 @@
 
     <macro name="requirements">
         <requirements>
-            <requirement type="package" version="2.10.3">sra-tools</requirement>
+            <requirement type="package" version="@VERSION@">sra-tools</requirement>
             <requirement type="package" version="2.3.4">pigz</requirement>
             <yield/>
         </requirements>
     </macro>
+    <macro name="configfile_hack">
+        <configfiles>
+            <configfile name="user_settings_mkfg"><![CDATA[
+/LIBS/GUID = "3cdc38d0-711a-49ce-9536-f544eaf69eec"
+/config/default = "false"
+/libs/temp_cache = "."
+/tools/prefetch/download_to_cache = "false"
+            ]]></configfile>
+        </configfiles>
+    </macro>
     <macro name="sanitize_query">
         <sanitizer>
             <valid initial="string.printable">