Mercurial > repos > mvdbeek > test_sra

changeset 2:2c5483e80fb7 draft

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planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
author mvdbeek
date Fri, 14 Aug 2015 12:48:14 -0400
parents 29892b1d24b9
children fb21b2e48a1e
files bam_dump.xml fastq_dump.xml sam_dump.xml sra_pileup.xml tool_dependencies.xml
diffstat 5 files changed, 23 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/bam_dump.xml	Fri Aug 14 12:29:26 2015 -0400
+++ b/bam_dump.xml	Fri Aug 14 12:48:14 2015 -0400
@@ -73,7 +73,7 @@
     <exit_code range="127" level="fatal" description="Could not locate sam-dump and/or samtools binary"/>
   </stdio>
   <requirements>
-    <requirement type="package" version="2.4.5">sra_toolkit</requirement>
+    <requirement type="package" version="2.5.2">sra_toolkit</requirement>
     <requirement type="package" version="1.2">samtools</requirement>
   </requirements>
   <tests>
--- a/fastq_dump.xml	Fri Aug 14 12:29:26 2015 -0400
+++ b/fastq_dump.xml	Fri Aug 14 12:48:14 2015 -0400
@@ -112,7 +112,7 @@
     <exit_code range="127" level="fatal" description="Could not locate fastq-dump binary"/>
   </stdio>
   <requirements>
-    <requirement type="package" version="2.4.5">sra_toolkit</requirement>
+    <requirement type="package" version="2.5.2">sra_toolkit</requirement>
   </requirements>
   <tests>
     <test>
--- a/sam_dump.xml	Fri Aug 14 12:29:26 2015 -0400
+++ b/sam_dump.xml	Fri Aug 14 12:48:14 2015 -0400
@@ -70,7 +70,7 @@
     <data name="output" format="sam"/>
   </outputs>
   <requirements>
-    <requirement type="package" version="2.4.5">sra_toolkit</requirement>
+    <requirement type="package" version="2.5.2">sra_toolkit</requirement>
   </requirements>
   <tests>
     <test>
--- a/sra_pileup.xml	Fri Aug 14 12:29:26 2015 -0400
+++ b/sra_pileup.xml	Fri Aug 14 12:48:14 2015 -0400
@@ -40,7 +40,7 @@
     <data format="pileup" name="output"/>
   </outputs>
   <requirements>
-    <requirement type="package" version="2.4.5">sra_toolkit</requirement>
+    <requirement type="package" version="2.5.2">sra_toolkit</requirement>
   </requirements>
   <tests>
     <test>
--- a/tool_dependencies.xml	Fri Aug 14 12:29:26 2015 -0400
+++ b/tool_dependencies.xml	Fri Aug 14 12:48:14 2015 -0400
@@ -1,15 +1,30 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="sra_toolkit" version="2.4.5">
+  <package name="sra_toolkit" version="2.5.2">
     <install version="1.0">
       <actions>
         <action type="make_directory">src</action>
         <action type="make_directory">build</action>
         <action type="change_directory">src</action>
+        <action type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
         <action type="shell_command">
-            git clone https://github.com/mdshw5/sra-tools.git
-            git clone https://github.com/mdshw5/ncbi-vdb.git
-            git clone https://github.com/mdshw5/ngs.git
+            tar -xf 2.5.2.tar.gz
+            rm 2.5.2.tar.gz
+            mv sra-tools-2.5.2 sra-tools
+        </action>
+        <action type="download_by_url">https://github.com/ncbi/ngs/archive/1.1.3.tar.gz</action>
+        <action type="shell_command">
+            tar -xf 1.1.3.tar.gz
+            rm 1.1.3.tar.gz
+            mv ngs-1.1.3 ngs      
+        </action>
+        <action type="download_by_url">https://github.com/ncbi/ncbi-vdb/archive/2.5.2.tar.gz</action>
+        <action type="shell_command">
+            tar -xf 2.5.2.tar.gz
+            rm 2.5.2.tar.gz
+            mv  ncbi-vdb-2.5.2  ncbi-vdb      
+        </action>
+        <action type="shell_command">
             LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib
             cd $INSTALL_DIR/src/ncbi-vdb
             ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build