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comparison tools/ncbi_blast_plus/blast2go.txt @ 2:e88a3246520e

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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
comparison
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1:0f159cf346c8 2:e88a3246520e
53 latest server IP address and database name given on the Blast2GO website. 53 latest server IP address and database name given on the Blast2GO website.
54 These files can be anywhere accessable to the Galaxy Unix user, we put them 54 These files can be anywhere accessable to the Galaxy Unix user, we put them
55 under /opt/b2g4pipe with the JAR file etc. 55 under /opt/b2g4pipe with the JAR file etc.
56 56
57 You must tell Galaxy about these Blast2GO property files so that they can be 57 You must tell Galaxy about these Blast2GO property files so that they can be
58 offered to the user. Create the file tool-data/blast2go.loc under the Galaxy 58 offered to the user. Copy file blast2go.loc.sample to tool-data/blast2go.loc
59 folder. This must be plain text, tab separated, with three columns: 59 under the Galaxy folder and edit this to match your installation. This must
60 be plain text, tab separated, with three columns:
60 61
61 (1) ID for the setup, e.g. Spain_2010_May 62 (1) ID for the setup, e.g. Spain_2010_May
62 (2) Description for the setup, e.g. Database in Spain (May 2010) 63 (2) Description for the setup, e.g. Database in Spain (May 2010)
63 (3) Properties filename for the setup, e.g. /opt/b2g4pipe/Spain_2010_May.properties 64 (3) Properties filename for the setup, e.g. /opt/b2g4pipe/Spain_2010_May.properties
64 65
79 v0.0.2 - Documentation clarifications, e.g. concatenated BLAST XML is allowed. 80 v0.0.2 - Documentation clarifications, e.g. concatenated BLAST XML is allowed.
80 - Fixed error handler in wrapper script (for when b2g4pipe fails). 81 - Fixed error handler in wrapper script (for when b2g4pipe fails).
81 - Reformats the XML to use old NCBI-style concatenated BLAST XML since 82 - Reformats the XML to use old NCBI-style concatenated BLAST XML since
82 b2g4pipe crashes with heap space error on with large files using 83 b2g4pipe crashes with heap space error on with large files using
83 current NCBI output. 84 current NCBI output.
85 v0.0.3 - Include sample loc file, tool-data/blast2go.loc.sample
84 86
85 87
86 Developers 88 Developers
87 ========== 89 ==========
88 90
90 http://bitbucket.org/peterjc/galaxy-central/src/tools 92 http://bitbucket.org/peterjc/galaxy-central/src/tools
91 93
92 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball I use 94 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball I use
93 the following command from the Galaxy root folder: 95 the following command from the Galaxy root folder:
94 96
95 $ tar -czf blast2go.tar.gz tools/ncbi_blast_plus/blast2go.xml tools/ncbi_blast_plus/blast2go.py tools/ncbi_blast_plus/blast2go.txt 97 $ 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
96 98
97 Check this worked: 99 Check this worked:
98 100
99 $ tar -tzf blast2go.tar.gz 101 $ tar -tzf blast2go.tar.gz
100 tools/ncbi_blast_plus/blast2go.xml 102 tools/ncbi_blast_plus/blast2go.xml
101 tools/ncbi_blast_plus/blast2go.py 103 tools/ncbi_blast_plus/blast2go.py
102 tools/ncbi_blast_plus/blast2go.txt 104 tools/ncbi_blast_plus/blast2go.txt
105 tool-data/blast2go.loc.sample
103 106
104 107
105 Licence (MIT/BSD style) 108 Licence (MIT/BSD style)
106 ======================= 109 =======================
107 110