Mercurial > repos > iuc > package_blast_plus_2_2_28
annotate tool_dependencies.xml @ 3:767d3d3b5cbe draft
Define BLAST_ROOT_DIR env var on older BLAST+ packages
| author | peterjc |
|---|---|
| date | Wed, 30 Sep 2015 09:20:36 -0400 |
| parents | f5493f01911b |
| children | 222036f7cab6 |
| rev | line source |
|---|---|
| 1 | 1 <?xml version='1.0' encoding='utf-8'?> |
| 0 | 2 <tool_dependency> |
| 3 <package name="blast+" version="2.2.28"> | |
| 4 <install version="1.0"> | |
| 1 | 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> | |
| 2 | 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> | |
| 1 | 50 <action type="shell_command">uname</action> |
| 51 <action type="shell_command">arch</action> | |
| 2 | 52 <action type="shell_command">echo "Please report this via https://github.com/peterjc/galaxy_blast/issues - thank you!"</action> |
| 1 | 53 <action type="shell_command">false</action> |
| 2 | 54 <!-- The 'false' command will return an error, so Galaxy should treat this as a failed install --> |
| 1 | 55 </actions> |
| 56 <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. --> | |
| 0 | 57 <action type="set_environment"> |
| 58 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> | |
|
3
767d3d3b5cbe
Define BLAST_ROOT_DIR env var on older BLAST+ packages
peterjc
parents:
2
diff
changeset
|
59 <environment_variable name="BLAST_ROOT_DIR" action="set_to">$INSTALL_DIR</environment_variable> |
| 0 | 60 </action> |
| 1 | 61 </actions_group> |
| 0 | 62 </install> |
| 63 <readme> | |
| 64 Downloads the precompiled 32bit Linux, 64bit Linux, or Mac OS X BLAST+ | |
| 2 | 65 binaries from the NCBI, which is faster than performing a local compilation, |
| 0 | 66 avoids any issues with build dependencies, and is more reproducible between |
| 67 installations as there is no variability from the compiler or library versions. | |
| 68 | |
| 69 For more details, see: | |
| 70 http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download | |
| 71 </readme> | |
| 72 </package> | |
| 73 </tool_dependency> |