Mercurial > repos > peterjc > blast2go
changeset 2:e88a3246520e
Uploaded v0.0.3 which adds tool-data/blast2go.loc.sample example settings file
| author | peterjc |
|---|---|
| date | Tue, 02 Aug 2011 09:20:52 -0400 |
| parents | 0f159cf346c8 |
| children | a5594772282c |
| files | tool-data/blast2go.loc.sample tools/ncbi_blast_plus/blast2go.txt tools/ncbi_blast_plus/blast2go.xml |
| diffstat | 3 files changed, 22 insertions(+), 4 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/blast2go.loc.sample Tue Aug 02 09:20:52 2011 -0400 @@ -0,0 +1,15 @@ +# 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
--- a/tools/ncbi_blast_plus/blast2go.txt Tue Jun 07 16:29:28 2011 -0400 +++ b/tools/ncbi_blast_plus/blast2go.txt Tue Aug 02 09:20:52 2011 -0400 @@ -55,8 +55,9 @@ 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) @@ -81,6 +82,7 @@ - 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 Developers @@ -92,7 +94,7 @@ 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 tool-data/blast2go.loc.sample Check this worked: @@ -100,6 +102,7 @@ tools/ncbi_blast_plus/blast2go.xml tools/ncbi_blast_plus/blast2go.py tools/ncbi_blast_plus/blast2go.txt +tool-data/blast2go.loc.sample Licence (MIT/BSD style)
--- a/tools/ncbi_blast_plus/blast2go.xml Tue Jun 07 16:29:28 2011 -0400 +++ b/tools/ncbi_blast_plus/blast2go.xml Tue Aug 02 09:20:52 2011 -0400 @@ -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