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changeset 12:fafc7f75d7ed draft

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Uploaded v0.0.8 preview 8, renamed README file, MIT licence, citation information
author peterjc
date Wed, 11 Sep 2013 05:55:24 -0400
parents f3a61c2cf309
children fd0c284a245c
files tools/blast2go/README.rst tools/blast2go/blast2go.txt tools/blast2go/blast2go.xml tools/blast2go/repository_dependencies.xml
diffstat 4 files changed, 215 insertions(+), 192 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/blast2go/README.rst	Wed Sep 11 05:55:24 2013 -0400
@@ -0,0 +1,198 @@
+Galaxy wrapper for Blast2GO for pipelines, b2g4pipe
+===================================================
+
+This wrapper is copyright 2011-2013 by Peter Cock, The James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below (MIT licence).
+
+This is a wrapper for the command line Java tool b2g4pipe v2.5,
+Blast2GO for pipelines. It is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go
+
+
+References
+==========
+
+Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
+
+S. Götz et al. (2008).
+High-throughput functional annotation and data mining with the Blast2GO suite.
+Nucleic Acids Res. 36(10):3420–3435.
+http://dx.doi.org/10.1093/nar/gkn176
+
+A. Conesa and S. Götz (2008).
+Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics.
+International Journal of Plant Genomics. 619832.
+http://dx.doi.org/10.1155/2008/619832
+
+A. Conesa et al. (2005).
+Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research.
+Bioinformatics 21:3674-3676.
+http://dx.doi.org/10.1093/bioinformatics/bti610
+
+See also http://www.blast2go.org/
+
+
+Automated Installation
+======================
+
+Installation via the Galaxy Tool Shed should take care of the Galaxy side of
+things, including the dependency on 'blast_datatypes' which defines the
+'blastxml' file format. However, you will also probably need to configure
+the Blast2GO property file(s), for example if you have a local Blast2GO
+database (which we recommend for speed).
+
+
+Manual 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). At the time of writing,
+the current version is b2g4pipe v2.5 which is available here:
+
+* http://www.blast2go.com/data/blast2go/b2g4pipe_v2.5.zip
+
+You can change the path by setting the B2G4PIP environement variable to
+the desired folder, but by default the script looks for the JAR file here::
+
+    /opt/b2g4pipe_v2.5/blast2go.jar
+
+To install the wrapper manually, first install 'blast_datatypes', then
+copy or move the following files under the Galaxy tools folder, e.g. in a
+tools/blast2go/ folder:
+
+* blast2go.xml (the Galaxy tool definition)
+* blast2go.py (the Python wrapper script)
+* README.rst (this file)
+
+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="blast2go/blast2go.xml" />
+
+If you wish to run the unit tests, also add this to tools_conf.xml.sample
+and move/copy the test-data files under Galaxy's test-data folder. Then::
+
+    $ ./run_functional_tests.sh -id blast2go
+
+
+Configuration
+=============
+
+As part of setting up b2g4pipe you will need to setup one or more Blast2GO
+property files which tell the tool which database to use etc. The example
+b2gPipe.properties provided with b2g4pipe is often out of date. The current
+server IP address and database name may given on the Blast2GO website, or
+can be found by running the latest GUI version via Java web-start, and
+looking under the tools/options menu. These property files can be anywhere
+accessable to the Galaxy Unix user, we put them with the JAR file etc.
+
+You must tell Galaxy about these Blast2GO property files so that they can be
+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_2012_August
+2. Description for the setup, e.g. Database in Spain (August 2012)
+3. Properties filename for the setup, e.g. Spain_2012_August.properties
+   relative to the main JAR file, or with a full path
+   e.g. /opt/b2g4pipe/Spain_2012_August.properties
+
+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
+the default setting, include it as the first line in your blast2go.loc file.
+
+Consult the Blast2GO documentation for details about the property files and
+setting up a local MySQL Blast2GO database.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial public release
+v0.0.2  - Documentation clarifications, e.g. concatenated BLAST XML is allowed.
+        - Fixed error handler in wrapper script (for when b2g4pipe fails).
+        - 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)
+v0.0.5  - Quote arguments in case of spaces in filenames (internal change)
+        - Last release supporting b2g4pipe v2.3.5
+v0.0.6  - Support for b2g4pipe v2.5 instead of v2.3.5
+          - Now invoked with a class path and es.blast2go.prog.B2GAnnotPipe
+            rather then simply calling the jar file
+          - Now uses the switch -annot instead of -a (this change breaks
+            support for b2g4pipe v2.3.5 unfortunately)
+        - Catch a few error messages and treat them explicitly as errors.
+v0.0.7  - Update output description in XML file (b2g4pipe v2.3.5 included
+         the sequence description, b2g4pipe v2.5 omits this).
+v0.0.8  - Automated installation via the Galaxy Tool Shed.
+        - Added unit test.
+        - Explain how to load the tabular file into the Blast2GO GUI.
+        - Link to Tool Shed added to help text and this documentation.
+        - Switch to standard MIT licence.
+        - Use reStructuredText for this README file.
+        - Updated citation information (Cock et al. 2013).
+======= ======================================================================
+
+
+Developers
+==========
+
+This script and related tools are being developed on the following hg branch:
+http://bitbucket.org/peterjc/galaxy-central/src/tools
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
+the following command from the Galaxy root folder::
+
+    $ tar -czf blast2go.tar.gz tools/blast2go/README.rst tools/blast2go/blast2go.xml tools/blast2go/blast2go.py tools/blast2go/repository_dependencies.xml tools/blast2go/tool_dependencies.xml tool-data/blast2go.loc.sample test-data/blastp_sample.xml test-data/blastp_sample.blast2go.tabular
+
+Check this worked::
+
+    $ tar -tzf blast2go.tar.gz
+    tools/blast2go/README.rst
+    tools/blast2go/blast2go.xml
+    tools/blast2go/blast2go.py
+    tools/blast2go/repository_dependencies.xml
+    tools/blast2go/tool_dependencies.xml
+    tool-data/blast2go.loc.sample
+    test-data/blastp_sample.xml
+    test-data/blastp_sample.blast2go.tabular
+
+
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+
+
+NOTE: This is the licence for the Galaxy Wrapper only. Blast2GO and
+associated data files are available and licenced separately.
--- a/tools/blast2go/blast2go.txt	Thu May 23 04:38:17 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,183 +0,0 @@
-Galaxy wrapper for Blast2GO for pipelines, b2g4pipe
-===================================================
-
-This wrapper is copyright 2011-2013 by Peter Cock, The James Hutton Institute
-(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
-See the licence text below.
-
-This is a wrapper for the command line Java tool b2g4pipe v2.5,
-Blast2GO for pipelines. It is available from the Galaxy Tool Shed at:
-http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go
-
-See also:
-
-S. Götz et al.
-High-throughput functional annotation and data mining with the Blast2GO suite.
-Nucleic Acids Res. 36(10):3420–3435, 2008.
-http://dx.doi.org/10.1093/nar/gkn176
-
-A. Conesa and S. Götz.
-Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics.
-Int. J. Plant Genomics. 619832, 2008.
-http://dx.doi.org/10.1155/2008/619832
-
-A. Conesa et al.
-Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research.
-Bioinformatics 21:3674-3676, 2005.
-http://dx.doi.org/10.1093/bioinformatics/bti610
-
-http://www.blast2go.org/
-
-
-Automated Installation
-======================
-
-Installation via the Galaxy Tool Shed should take care of the Galaxy side of
-things, including the dependency on 'blast_datatypes' which defines the
-'blastxml' file format. However, you will also probably need to configure
-the Blast2GO property file(s), for example if you have a local Blast2GO
-database (which we recommend for speed).
-
-
-Manual 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). At the time of writing,
-the current version is b2g4pipe v2.5 which is available here:
-
-http://www.blast2go.com/data/blast2go/b2g4pipe_v2.5.zip
-
-You can change the path by setting the B2G4PIP environement variable to
-the desired folder, but by default the script looks for the JAR file here:
-
-/opt/b2g4pipe_v2.5/blast2go.jar
-
-To install the wrapper manually, first install 'blast_datatypes', then
-copy or move the following files under the Galaxy tools folder, e.g. in a
-tools/blast2go/ folder:
-
-* blast2go.xml (the Galaxy tool definition)
-* blast2go.py (the Python wrapper script)
-* blast2go.txt (this README file)
-
-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="blast2go/blast2go.xml" />
-
-If you wish to run the unit tests, also add this to tools_conf.xml.sample
-and move/copy the test-data files under Galaxy's test-data folder. Then:
-
-$ ./run_functional_tests.sh -id blast2go
-
-
-Configuration
-=============
-
-As part of setting up b2g4pipe you will need to setup one or more Blast2GO
-property files which tell the tool which database to use etc. The example
-b2gPipe.properties provided with b2g4pipe is often out of date. The current
-server IP address and database name may given on the Blast2GO website, or
-can be found by running the latest GUI version via Java web-start, and
-looking under the tools/options menu. These property files can be anywhere
-accessable to the Galaxy Unix user, we put them with the JAR file etc.
-
-You must tell Galaxy about these Blast2GO property files so that they can be
-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_2012_August
-(2) Description for the setup, e.g. Database in Spain (August 2012)
-(3) Properties filename for the setup, e.g. Spain_2012_August.properties
-    relative to the main JAR file, or with a full path
-    e.g. /opt/b2g4pipe/Spain_2012_August.properties
-
-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
-the default setting, include it as the first line in your blast2go.loc file.
-
-Consult the Blast2GO documentation for details about the property files and
-setting up a local MySQL Blast2GO database.
-
-
-History
-=======
-
-v0.0.1 - Initial public release
-v0.0.2 - Documentation clarifications, e.g. concatenated BLAST XML is allowed.
-       - Fixed error handler in wrapper script (for when b2g4pipe fails).
-       - 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)
-v0.0.5 - Quote arguments in case of spaces in filenames (internal change)
-       - Last release supporting b2g4pipe v2.3.5
-v0.0.6 - Support for b2g4pipe v2.5 instead of v2.3.5
-          - Now invoked with a class path and es.blast2go.prog.B2GAnnotPipe
-            rather then simply calling the jar file
-          - Now uses the switch -annot instead of -a (this change breaks
-            support for b2g4pipe v2.3.5 unfortunately)
-       - Catch a few error messages and treat them explicitly as errors.
-v0.0.7 - Update output description in XML file (b2g4pipe v2.3.5 included
-         the sequence description, b2g4pipe v2.5 omits this).
-v0.0.8 - Automated installation via the Galaxy Tool Shed.
-       - Added unit test.
-       - Explain how to load the tabular file into the Blast2GO GUI.
-       - Link to Tool Shed added to help text and this documentation.
-
-
-Developers
-==========
-
-This script and related tools are being developed on the following hg branch:
-http://bitbucket.org/peterjc/galaxy-central/src/tools
-
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
-the following command from the Galaxy root folder:
-
-$ tar -czf blast2go.tar.gz tools/blast2go/blast2go.xml tools/blast2go/blast2go.py tools/blast2go/blast2go.txt tools/blast2go/repository_dependencies.xml tools/blast2go/tool_dependencies.xml tool-data/blast2go.loc.sample test-data/blastp_sample.xml test-data/blastp_sample.blast2go.tabular
-
-Check this worked:
-
-$ tar -tzf blast2go.tar.gz
-tools/blast2go/blast2go.xml
-tools/blast2go/blast2go.py
-tools/blast2go/blast2go.txt
-tools/blast2go/repository_dependencies.xml
-tools/blast2go/tool_dependencies.xml
-tool-data/blast2go.loc.sample
-test-data/blastp_sample.xml
-test-data/blastp_sample.blast2go.tabular
-
-
-Licence (MIT/BSD style)
-=======================
-
-Permission to use, copy, modify, and distribute this software and its
-documentation with or without modifications and for any purpose and
-without fee is hereby granted, provided that any copyright notices
-appear in all copies and that both those copyright notices and this
-permission notice appear in supporting documentation, and that the
-names of the contributors or copyright holders not be used in
-advertising or publicity pertaining to distribution of the software
-without specific prior permission.
-
-THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
-WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
-CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
-OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
-OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
-OR PERFORMANCE OF THIS SOFTWARE.
-
-NOTE: This is the licence for the Galaxy Wrapper only. Blast2GO and
-associated data files are available and licenced separately.
--- a/tools/blast2go/blast2go.xml	Thu May 23 04:38:17 2013 -0400
+++ b/tools/blast2go/blast2go.xml	Wed Sep 11 05:55:24 2013 -0400
@@ -86,22 +86,30 @@
 
 **References**
 
-S. Götz et al.
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
+
+S. Götz et al. (2008).
 High-throughput functional annotation and data mining with the Blast2GO suite.
-Nucleic Acids Res. 36(10):3420–3435, 2008.
+Nucleic Acids Res. 36(10):3420–3435.
 http://dx.doi.org/10.1093/nar/gkn176
 
-A. Conesa and S. Götz.
+A. Conesa and S. Götz (2008).
 Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics.
-Int. J. Plant Genomics. 619832, 2008.
+International Journal of Plant Genomics. 619832.
 http://dx.doi.org/10.1155/2008/619832
 
-A. Conesa et al.
+A. Conesa et al. (2005).
 Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research.
-Bioinformatics 21:3674-3676, 2005.
+Bioinformatics 21:3674-3676.
 http://dx.doi.org/10.1093/bioinformatics/bti610
 
-http://www.blast2go.com/
+See also http://www.blast2go.com/
 
 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go
--- a/tools/blast2go/repository_dependencies.xml	Thu May 23 04:38:17 2013 -0400
+++ b/tools/blast2go/repository_dependencies.xml	Wed Sep 11 05:55:24 2013 -0400
@@ -1,5 +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 (and test) tool shed is v0.0.14 which added BLAST databases -->
 <repository changeset_revision="f9a7783ed7b6" name="blast_datatypes" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-</repositories>
\ No newline at end of file
+</repositories>