Mercurial > repos > peterjc > ncbi_blast_plus
changeset 25:949fa0294c0d draft
Uploaded v0.0.20pre16, depend on package_blast_plus_2_2_26
| author | peterjc |
|---|---|
| date | Wed, 07 Aug 2013 13:09:24 -0400 |
| parents | 5693417851ec |
| children | 946749c8605f |
| files | ncbi_blast_plus/README.rst ncbi_blast_plus/repository_dependencies.xml ncbi_blast_plus/tool_dependencies.xml |
| diffstat | 3 files changed, 2 insertions(+), 31 deletions(-) [+] |
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--- a/ncbi_blast_plus/README.rst Tue Aug 06 12:04:54 2013 -0400 +++ b/ncbi_blast_plus/README.rst Wed Aug 07 13:09:24 2013 -0400 @@ -115,7 +115,6 @@ - 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 uses the NCBI supplied pre-compiled binaries. ======= ======================================================================
--- a/ncbi_blast_plus/repository_dependencies.xml Tue Aug 06 12:04:54 2013 -0400 +++ b/ncbi_blast_plus/repository_dependencies.xml Wed Aug 07 13:09:24 2013 -0400 @@ -1,5 +1,4 @@ <?xml version="1.0"?> <repositories description="This requires the BLAST datatype definitions (e.g. the BLAST XML format)."> -<!-- Revision 4:f9a7783ed7b6 on the main (and test) tool shed is v0.0.14 which added BLAST databases --> -<repository changeset_revision="f9a7783ed7b6" name="blast_datatypes" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="a44a7a5456e1" name="blast_datatypes" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </repositories>
--- a/ncbi_blast_plus/tool_dependencies.xml Tue Aug 06 12:04:54 2013 -0400 +++ b/ncbi_blast_plus/tool_dependencies.xml Wed Aug 07 13:09:24 2013 -0400 @@ -1,33 +1,6 @@ <?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</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> -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&PAGE_TYPE=BlastDocs&DOC_TYPE=Download - </readme> + <repository changeset_revision="733eee977fb8" name="package_blast_plus_2_2_26" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>