| Previous changeset 18:cc1416954958 (2013-05-27) Next changeset 20:688f3fb09a6a (2013-07-30) |
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Commit message:
Uploaded v0.0.20 preview 10. Auto install of 64 bit Linux binaries was working, but reverting to local compile for cross-platform support. |
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modified:
tools/ncbi_blast_plus/ncbi_blast_plus.txt tools/ncbi_blast_plus/tool_dependencies.xml |
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| diff -r cc1416954958 -r c1a6e5aefee0 tools/ncbi_blast_plus/ncbi_blast_plus.txt --- a/tools/ncbi_blast_plus/ncbi_blast_plus.txt Mon May 27 11:42:33 2013 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blast_plus.txt Wed May 29 10:03:48 2013 -0400 |
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| @@ -105,8 +105,6 @@ fall-back in case the return code is not set properly). - Clearer naming of output files. v0.0.20 - Added unit tests for BLASTN and TBLASTX. - - Automatic installation via the Tool Shed now uses the NCBI provided - precompiled binaries for 64bit Linux, rather than compiling locally. - Fallback on ElementTree if cElementTree missing in XML to tabular. - Link to Tool Shed added to help text and this documentation. - Tweak dependency on blast_datatypes to also work on Test Tool Shed |
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| diff -r cc1416954958 -r c1a6e5aefee0 tools/ncbi_blast_plus/tool_dependencies.xml --- a/tools/ncbi_blast_plus/tool_dependencies.xml Mon May 27 11:42:33 2013 -0400 +++ b/tools/ncbi_blast_plus/tool_dependencies.xml Wed May 29 10:03:48 2013 -0400 |
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| @@ -3,27 +3,16 @@ <package name="blast+" version="2.2.26+"> <install version="1.0"> <actions> - <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-x64-linux.tar.gz</action> - <action type="move_directory_files"> - <!-- Galaxy will have changed directory into ncbi-blast-2.2.26+/ --> - <source_directory>bin</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> + <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-src.tar.gz</action> + <action type="shell_command">cd c++ && ./configure --prefix=$INSTALL_DIR && make && make install</action> <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> -Downloads the precompiled 64bit Linux 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. - -If/when the Galaxy installation framework allows for 32bit versus 64bit, -or different operating system, the NCBI binaries cover the main cases. - -For more details, see: +Downloads and compiles BLAST+ from the NCBI, which assumes you have +all the required build dependencies installed. See: http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download </readme> </package> |