Mercurial > repos > peterjc > ncbi_blast_plus

changeset 24:5693417851ec draft

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Uploaded v0.0.20pre15, try platform selection installation via shell commands.
author peterjc
date Tue, 06 Aug 2013 12:04:54 -0400
parents 2c70fed75e57
children 949fa0294c0d
files ncbi_blast_plus/README.rst ncbi_blast_plus/tool_dependencies.xml
diffstat 2 files changed, 19 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- a/ncbi_blast_plus/README.rst	Mon Aug 05 16:03:58 2013 -0400
+++ b/ncbi_blast_plus/README.rst	Tue Aug 06 12:04:54 2013 -0400
@@ -115,8 +115,7 @@
         - Tweak dependency on blast_datatypes to also work on Test Tool Shed
         - Adopted standard MIT License.
         - Development moved to GitHub, https://github.com/peterjc/galaxy_blast
-        - Auto-installation tries to use the NCBI supplied binaries, falling
-          back on local compilation from source if required (Dave Bouvier).
+        - Auto-installation uses the NCBI supplied pre-compiled binaries.
 ======= ======================================================================
 
 
--- a/ncbi_blast_plus/tool_dependencies.xml	Mon Aug 05 16:03:58 2013 -0400
+++ b/ncbi_blast_plus/tool_dependencies.xml	Tue Aug 06 12:04:54 2013 -0400
@@ -3,23 +3,30 @@
     <package name="blast+" version="2.2.26+">
         <install version="1.0">
             <actions>
-                <action type="download_binary">
-                    <url_template os="darwin">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-universal-macosx.tar.gz</url_template>
-                    <url_template os="linux" architecture="x86_64">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-x64-linux.tar.gz</url_template>
-                    <url_template os="linux" architecture="i386">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-ia32-linux.tar.gz</url_template>
-                    <url_template os="linux" architecture="i686">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-ia32-linux.tar.gz</url_template>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                 </action>
-                <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-src.tar.gz</action>
-                <action type="shell_command">cd c++ &amp;&amp; ./configure --prefix=$INSTALL_DIR/ncbi-blast-2.2.26+ &amp;&amp; make &amp;&amp; make install</action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+		<!-- arch under Linux 32bit includes some variants like i386 and i686, so use as default -->
+                <action type="shell_command">if [[ "$(uname)" == "Linux" ]]; then export FILENAME="ncbi-blast-2.2.26+-ia32-linux.tar.gz"; fi</action>
+		<action type="shell_command">if [[ "$(arch)" == "x86_64" ]]; then export FILENAME="ncbi-blast-2.2.26+-x64-linux.tar.gz"; fi</action>
+                <action type="shell_command">if [[ "$(uname)" == "Darwin" ]]; then export FILENAME="ncbi-blast-2.2.26+-universal-macosx.tar.gz"; fi</action>
+		<!-- now download and unzip it, assuming can't use $FILENAME in the Tool Shed action? -->
+		<action type="shell_command">wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME</action>
+		<action type="shell_command">tar -zxvf $FILENAME</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>
-These links provide information for building the NCBI Blast+ package in most environments.
+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.
 
-System requirements
+For more details, see:
 http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs&amp;DOC_TYPE=Download
         </readme>
     </package>