Mercurial > repos > matt-shirley > ncbi_sra_toolkit

changeset 25:393a04ec0fa9

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Update tool requirement versions.
author Matt Shirley <mdshw5@gmail.com>
date Mon, 30 Mar 2015 21:57:40 -0400
parents 22d9fe442c50
children 7d80b2b24270
files fastq_dump.xml sam_dump.xml sra_pileup.xml tool_dependencies.xml
diffstat 4 files changed, 10 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/fastq_dump.xml	Mon Mar 30 21:33:57 2015 -0400
+++ b/fastq_dump.xml	Mon Mar 30 21:57:40 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="2.3.4-2">sra_toolkit</requirement>
+    <requirement type="package" version="2.4.5">sra_toolkit</requirement>
   </requirements>
   <help>
     This tool extracts reads from SRA archives using fastq-dump.
--- a/sam_dump.xml	Mon Mar 30 21:33:57 2015 -0400
+++ b/sam_dump.xml	Mon Mar 30 21:57:40 2015 -0400
@@ -88,7 +88,7 @@
     </data>
   </outputs>
   <requirements>
-    <requirement type="package" version="2.3.4-2">sra_toolkit</requirement>
+    <requirement type="package" version="2.4.5">sra_toolkit</requirement>
   </requirements>
   <help>
     This tool extracts reads from sra archives using sam-dump.
--- a/sra_pileup.xml	Mon Mar 30 21:33:57 2015 -0400
+++ b/sra_pileup.xml	Mon Mar 30 21:57:40 2015 -0400
@@ -1,6 +1,6 @@
 <tool id="sra_pileup" name="Generate pileup format" version="1.1.1">
   <description> from NCBI sra.</description>
-  <command>sra-pileup --log-level fatal 
+  <command>sra-pileup --log-level fatal
     #if str( $region ) != "":
       --aligned-region $region
     #end if
@@ -10,7 +10,7 @@
     #if $input.input_select == "file":
       $input.file
     #elif $input.input_select == "accession_number":
-      $input.accession 
+      $input.accession
     #elif $input.input_select == "text":
       `cat $input.text`
     #end if
@@ -40,11 +40,11 @@
     <data format="pileup" name="output"/>
   </outputs>
   <requirements>
-    <requirement type="package" version="2.3.3-3">sra_toolkit</requirement>
+    <requirement type="package" version="2.4.5">sra_toolkit</requirement>
   </requirements>
   <help>
-    This tool produces pileup format from sra archives using sra-pileup. 
-    Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. 
+    This tool produces pileup format from sra archives using sra-pileup.
+    Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
     The sra-pileup program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
     Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
   </help>
--- a/tool_dependencies.xml	Mon Mar 30 21:33:57 2015 -0400
+++ b/tool_dependencies.xml	Mon Mar 30 21:57:40 2015 -0400
@@ -26,7 +26,9 @@
             cd $INSTALL_DIR/bin
             ./vdb-config -s "cache-enabled = false"
         </action>
-        <action type="set_environment"><environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable></action>
+        <action type="set_environment">
+            <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+        </action>
       </actions>
     </install>
     <readme>