Mercurial > repos > peterjc > blast2go
changeset 2:5cb24d07c316 draft
Uploaded v0.0.4 with explicit dependency on 'blast_datatypes' for 'blastxml' format definition. No functional changes.
| author | peterjc |
|---|---|
| date | Fri, 22 Feb 2013 09:13:27 -0500 |
| parents | 7b53cc52e7ed |
| children | 7602de1e7f32 |
| files | tool-data/blast2go.loc.sample tools/ncbi_blast_plus/blast2go.py tools/ncbi_blast_plus/blast2go.txt tools/ncbi_blast_plus/blast2go.xml tools/ncbi_blast_plus/repository_dependencies.xml |
| diffstat | 5 files changed, 49 insertions(+), 13 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/blast2go.loc.sample Fri Feb 22 09:13:27 2013 -0500 @@ -0,0 +1,16 @@ +# This is a three column tab separated file to define the properties +# file (settings) to be offered for Blast2GO for Pipelines (b2g4pipe). +# +# Column 1 - ID, string that Galaxy will save in its database +# Column 2 - Human readable name, Galaxy will show this in the UI +# Column 3 - Filename, Galaxy will use this when calling the tool +# +# Probably the most important setting in the properties file is the +# Blast2GO database to use. Currently b2g4pipe v2.3.5 ships with an +# old configuration so consult http://blast2go.org for the latest +# public database they host in Spain. We also strongly recommend +# configuring a local Blast2GO database. +# +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 Jun 07 15:51:46 2011 -0400 +++ b/tools/ncbi_blast_plus/blast2go.py Fri Feb 22 09:13:27 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 Jun 07 15:51:46 2011 -0400 +++ b/tools/ncbi_blast_plus/blast2go.txt Fri Feb 22 09:13:27 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" /> @@ -55,14 +64,15 @@ under /opt/b2g4pipe with the JAR file etc. You must tell Galaxy about these Blast2GO property files so that they can be -offered to the user. Create the file tool-data/blast2go.loc under the Galaxy -folder. This must be plain text, tab separated, with three columns: +offered to the user. Copy file blast2go.loc.sample to tool-data/blast2go.loc +under the Galaxy folder and edit this to match your installation. This must +be plain text, tab separated, with three columns: (1) ID for the setup, e.g. Spain_2010_May (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 @@ -81,6 +91,9 @@ - Reformats the XML to use old NCBI-style concatenated BLAST XML since 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 @@ -92,7 +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 +$ 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: @@ -100,6 +113,8 @@ 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 Licence (MIT/BSD style)
--- a/tools/ncbi_blast_plus/blast2go.xml Tue Jun 07 15:51:46 2011 -0400 +++ b/tools/ncbi_blast_plus/blast2go.xml Fri Feb 22 09:13:27 2013 -0500 @@ -1,4 +1,4 @@ -<tool id="blast2go" name="Blast2GO" version="0.0.2"> +<tool id="blast2go" name="Blast2GO" version="0.0.3"> <description>Maps BLAST results to GO annotation terms</description> <command interpreter="python"> blast2go.py $xml ${prop.fields.path} $tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/repository_dependencies.xml Fri Feb 22 09:13:27 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>