Mercurial > repos > peterjc > blast2go
changeset 3:a5594772282c draft
Uploaded v0.0.4 with explicit dependency on 'blast_datatypes' for 'blastxml' format definition.
No functional changes.
| author | peterjc |
|---|---|
| date | Fri, 08 Feb 2013 10:33:50 -0500 |
| parents | e88a3246520e |
| children | c8c04cd07ca0 |
| files | tool-data/blast2go.loc.sample tools/ncbi_blast_plus/blast2go.py tools/ncbi_blast_plus/blast2go.txt tools/ncbi_blast_plus/repository_dependencies.xml |
| diffstat | 4 files changed, 28 insertions(+), 10 deletions(-) [+] |
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--- a/tool-data/blast2go.loc.sample Tue Aug 02 09:20:52 2011 -0400 +++ b/tool-data/blast2go.loc.sample Fri Feb 08 10:33:50 2013 -0500 @@ -13,3 +13,4 @@ # Local_2011_May Local database (May 2011) /opt/b2g4pipe/Local_2011_May.properties Spain_2010_May Database in Spain (May 2010) /opt/b2g4pipe/Spain_2010_May.properties +Spain_2011_June Database in Spain (June 2011) /opt/b2g4pipe/Spain_2011_June.properties
--- a/tools/ncbi_blast_plus/blast2go.py Tue Aug 02 09:20:52 2011 -0400 +++ b/tools/ncbi_blast_plus/blast2go.py Fri Feb 08 10:33:50 2013 -0500 @@ -6,9 +6,9 @@ * Blast2GO properties filename (settings file) * Output tabular filename -Sadly b2g4pipe v2.3.5 cannot cope with current style large BLAST XML -files (e.g. from BLAST 2.2.25+), so we have to reformat these to -avoid it crashing with a Java heap space OutOfMemoryError. +Sadly b2g4pipe (at least v2.3.5 to v2.5.0) cannot cope with current +style large BLAST XML files (e.g. from BLAST 2.2.25+), so we reformat +these to avoid it crashing with a Java heap space OutOfMemoryError. As part of this reformatting, we check for BLASTP or BLASTX output (otherwise raise an error), and print the query count.
--- a/tools/ncbi_blast_plus/blast2go.txt Tue Aug 02 09:20:52 2011 -0400 +++ b/tools/ncbi_blast_plus/blast2go.txt Fri Feb 08 10:33:50 2013 -0500 @@ -30,20 +30,29 @@ Installation ============ +The main dependency is b2g4pipe which must be installed manually. Also we +strongly recommend installing a local Blast2GO database as well (see the +intructions below about the blast2go.loc file). + You can change the path by editing the definition near the start of the Python script blast2go.py, but by default it expects the underlying tool to be here: -/opt/b2g4pip/blast2go.jar +/opt/b2g4pipe/blast2go.jar + -To install the wrapper copy or move the following files under the Galaxy tools -folder, e.g. in the tools/ncbi_blast_blast folder: +Installation of the Galaxy wrapper should work automatically via the Galaxy +Tool Shed, including the dependency on 'blast_datatypes' for the 'blastxml' +file format definition. To install the wrapper manually, first install +'blast_datatypes', then copy or move the following files under the Galaxy +tools folder, e.g. in the tools/ncbi_blast_blast folder: * blast2go.xml (the Galaxy tool definition) * blast2go.py (the Python wrapper script) * blast2go.txt (this README file) -You will also need to modify the tools_conf.xml file to tell Galaxy to offer the -tool. We suggest putting it next to the NCBI BLAST+ wrappers. Just add the line: +For a manual installation of the wrapper you will also need to modify the +tools_conf.xml file to tell Galaxy to offer the tool. We suggest putting +it next to the NCBI BLAST+ wrappers. Just add the line: <tool file="ncbi_blast_plus/blast2go.xml" /> @@ -63,7 +72,7 @@ (2) Description for the setup, e.g. Database in Spain (May 2010) (3) Properties filename for the setup, e.g. /opt/b2g4pipe/Spain_2010_May.properties -Avoid including "Blast2GO" in the description (column 2) as this will be +Avoid including "Blast2GO" in the description (column 2) as this text will be included in the automatically assigned output dataset name. The blast2go.loc file allows you to customise the database setup. If for example you have a local Blast2GO server running (which we recommend for speed), and you want this to be @@ -83,6 +92,8 @@ b2g4pipe crashes with heap space error on with large files using current NCBI output. v0.0.3 - Include sample loc file, tool-data/blast2go.loc.sample +v0.0.4 - Include repository_dependencies.xml file for 'blastxml' format + (previously included in the core Galaxy installation) Developers @@ -94,7 +105,7 @@ For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball I use the following command from the Galaxy root folder: -$ tar -czf blast2go.tar.gz tools/ncbi_blast_plus/blast2go.xml tools/ncbi_blast_plus/blast2go.py tools/ncbi_blast_plus/blast2go.txt tool-data/blast2go.loc.sample +$ tar -czf blast2go.tar.gz tools/ncbi_blast_plus/blast2go.xml tools/ncbi_blast_plus/blast2go.py tools/ncbi_blast_plus/blast2go.txt tools/ncbi_blast_plus/repository_dependencies.xml tool-data/blast2go.loc.sample Check this worked: @@ -102,6 +113,7 @@ tools/ncbi_blast_plus/blast2go.xml tools/ncbi_blast_plus/blast2go.py tools/ncbi_blast_plus/blast2go.txt +tools/ncbi_blast_plus/repository_dependencies.xml tool-data/blast2go.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/repository_dependencies.xml Fri Feb 08 10:33:50 2013 -0500 @@ -0,0 +1,5 @@ +<?xml version="1.0"?> +<repositories description="This requires the BLAST datatype definitions (e.g. the BLAST XML format)."> +<!-- Revision 4:f9a7783ed7b6 on the main tool shed is v0.0.14 which added BLAST databases --> +<repository toolshed="http://toolshed.g2.bx.psu.edu" name="blast_datatypes" owner="devteam" changeset_revision="f9a7783ed7b6" /> +</repositories>