Mercurial > repos > iuc > package_blast_plus_2_2_26

changeset 0:40c69b76b46e draft

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Uploaded using shell script solution to downloading appropriate binaries.
author iuc
date Fri, 30 Aug 2013 07:26:10 -0400
parents
children d3343fa55e9e
files tool_dependencies.xml
diffstat 1 files changed, 37 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Aug 30 07:26:10 2013 -0400
@@ -0,0 +1,37 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="blast+" version="2.2.26+">
+        <install version="1.0">
+            <actions>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                </action>
+                <!-- arch under Linux 32bit includes some variants like i386 and i686, so use as default -->
+                <action type="shell_command">
+                    if [[ "$(uname)" == "Linux" ]]; then export FILENAME="ncbi-blast-2.2.26+-ia32-linux.tar.gz"; fi &amp;&amp;
+                    if [[ "$(arch)" == "x86_64" ]]; then export FILENAME="ncbi-blast-2.2.26+-x64-linux.tar.gz"; fi &amp;&amp;
+                    if [[ "$(uname)" == "Darwin" ]]; then export FILENAME="ncbi-blast-2.2.26+-universal-macosx.tar.gz"; fi &amp;&amp;
+                    echo Fetching $FILENAME &amp;&amp;
+                    if [[ "$(uname)" == "Linux" ]]; then wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi &amp;&amp;
+                    if [[ "$(uname)" == "Darwin" ]]; then curl -O ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi &amp;&amp;
+                    tar -zxvf $FILENAME &amp;&amp;
+                    echo Downloaded and decompressed
+                </action>
+                <!-- move the binaries to the installation directory which is now on the $PATH -->
+                <action type="move_directory_files">
+                    <source_directory>ncbi-blast-2.2.26+/bin</source_directory>
+                    <destination_directory>$INSTALL_DIR</destination_directory>
+                </action>
+            </actions>
+        </install>
+        <readme>
+Downloads the precompiled 32bit Linux, 64bit Linux, or Mac OS X BLAST+
+binaries from the NCBI, which is faster than performing a local compliation,
+avoids any issues with build dependencies, and is more reproducible between
+installations as there is no variability from the compiler or library versions.
+
+For more details, see:
+http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs&amp;DOC_TYPE=Download
+        </readme>
+    </package>
+</tool_dependency>