Mercurial > repos > iuc > package_blast_plus_2_2_28

comparison tool_dependencies.xml @ 1:23b9ba41ad00 draft

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Updated to use os/arch specific actions
author peterjc
date Mon, 18 Nov 2013 05:42:38 -0500
parents ed85ca8e4295
children f5493f01911b
comparison
equal deleted inserted replaced
0:ed85ca8e4295 1:23b9ba41ad00
1 <?xml version="1.0"?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="blast+" version="2.2.28"> 3 <package name="blast+" version="2.2.28">
4 <install version="1.0"> 4 <install version="1.0">
5 <actions> 5 <actions_group>
6 <!-- Download the binaries for BLAST+ compatible with 64-bit OSX. -->
7 <actions os="darwin" architecture="x86_64">
8 <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/ncbi-blast-2.2.28+-universal-macosx.tar.gz</action>
9 <action type="move_directory_files">
10 <source_directory>bin</source_directory>
11 <destination_directory>$INSTALL_DIR</destination_directory>
12 </action>
13 </actions>
14 <!-- Download the binaries for BLAST+ compatible with 32-bit OSX. -->
15 <actions os="darwin" architecture="i386">
16 <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/ncbi-blast-2.2.28+-universal-macosx.tar.gz</action>
17 <action type="move_directory_files">
18 <source_directory>bin</source_directory>
19 <destination_directory>$INSTALL_DIR</destination_directory>
20 </action>
21 </actions>
22 <!-- Download the binaries for BLAST+ compatible with 64-bit Linux. -->
23 <actions os="linux" architecture="x86_64">
24 <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/ncbi-blast-2.2.28+-x64-linux.tar.gz</action>
25 <action type="move_directory_files">
26 <source_directory>bin</source_directory>
27 <destination_directory>$INSTALL_DIR</destination_directory>
28 </action>
29 </actions>
30 <!-- Download the binaries for BLAST+ compatible with 32-bit Linux (i386). -->
31 <actions os="linux" architecture="i386">
32 <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/ncbi-blast-2.2.28+-ia32-linux.tar.gz</action>
33 <action type="move_directory_files">
34 <source_directory>bin</source_directory>
35 <destination_directory>$INSTALL_DIR</destination_directory>
36 </action>
37 </actions>
38 <!-- Download the binaries for BLAST+ compatible with 32-bit Linux (i686). -->
39 <actions os="linux" architecture="i686">
40 <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/ncbi-blast-2.2.28+-ia32-linux.tar.gz</action>
41 <action type="move_directory_files">
42 <source_directory>bin</source_directory>
43 <destination_directory>$INSTALL_DIR</destination_directory>
44 </action>
45 </actions>
46 <!-- This actions tag is only processed if none of the above tags resulted in a successful installation. -->
47 <actions>
48 <action type="shell_command">echo ERROR: Automated installation on your operating system and CPU architecture combination is not yet supported.</action>
49 <action type="shell_command">echo Your machine details (the output from 'uname' and 'arch'):</action>
50 <action type="shell_command">uname</action>
51 <action type="shell_command">arch</action>
52 <action type="shell_command">echo Please report this via https://github.com/peterjc/galaxy_blast/issues - thank you!</action>
53 <action type="shell_command">false</action>
54 <!-- The 'false' command will return an error, so Galaxy should treat this as a failed install -->
55 </actions>
56 <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. -->
6 <action type="set_environment"> 57 <action type="set_environment">
7 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> 58 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
8 </action> 59 </action>
9 <!-- arch under Linux 32bit includes some variants like i386 and i686, so use as default --> 60 </actions_group>
10 <action type="shell_command">
11 if [[ "$(uname)" == "Linux" ]]; then export FILENAME="ncbi-blast-2.2.28+-ia32-linux.tar.gz"; fi &amp;&amp;
12 if [[ "$(arch)" == "x86_64" ]]; then export FILENAME="ncbi-blast-2.2.28+-x64-linux.tar.gz"; fi &amp;&amp;
13 if [[ "$(uname)" == "Darwin" ]]; then export FILENAME="ncbi-blast-2.2.28+-universal-macosx.tar.gz"; fi &amp;&amp;
14 echo Fetching $FILENAME &amp;&amp;
15 if [[ "$(uname)" == "Linux" ]]; then wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/$FILENAME; fi &amp;&amp;
16 if [[ "$(uname)" == "Darwin" ]]; then curl -O ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/$FILENAME; fi &amp;&amp;
17 tar -zxvf $FILENAME &amp;&amp;
18 echo Downloaded and decompressed
19 </action>
20 <!-- move the binaries to the installation directory which is now on the $PATH -->
21 <action type="move_directory_files">
22 <source_directory>ncbi-blast-2.2.28+/bin</source_directory>
23 <destination_directory>$INSTALL_DIR</destination_directory>
24 </action>
25 </actions>
26 </install> 61 </install>
27 <readme> 62 <readme>
28 Downloads the precompiled 32bit Linux, 64bit Linux, or Mac OS X BLAST+ 63 Downloads the precompiled 32bit Linux, 64bit Linux, or Mac OS X BLAST+
29 binaries from the NCBI, which is faster than performing a local compliation, 64 binaries from the NCBI, which is faster than performing a local compliation,
30 avoids any issues with build dependencies, and is more reproducible between 65 avoids any issues with build dependencies, and is more reproducible between