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changeset 4:c243e17fb224 draft

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Uploaded
author bgruening
date Fri, 07 Jun 2013 02:30:21 -0400
parents 702d9e042295
children bcfe8e0731f8
files augustus.xml readme.rst readme.txt
diffstat 3 files changed, 80 insertions(+), 82 deletions(-) [+]
line wrap: on
line diff
--- a/augustus.xml	Thu Jun 06 13:26:37 2013 -0400
+++ b/augustus.xml	Fri Jun 07 02:30:21 2013 -0400
@@ -151,7 +151,7 @@
             <output name="output" file="human_augustus_utr-on.gtf" ftype="gtf" />
         </test>
         <test>
-            <param name="input_genome" value="HS04636_augustus.fa" ftype="fasta" />
+            <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
             <param name="organism" value="human" />
             <param name="utr" value="--UTR=on" />
             <param name="gff" value="--gff3=on" />
@@ -162,10 +162,10 @@
             <param name="organism" value="arabidopsis" />
             <param name="singlestrand" value="--singlestrand=true" />
             <param name="mea" value="--mea=1" />
-            <output name="output" file="arabidopsis_augustus_utr-off_singlestrand-on_mea-on" ftype="gtf" />
+            <output name="output" file="arabidopsis_augustus_utr-off_singlestrand-on_mea-on.gtf" ftype="gtf" />
         </test>
         <test>
-            <param name="input_genome" value="HS04636_augustus.fa" ftype="fasta" />
+            <param name="input_genome" value="human_augustus.fa" ftype="fasta" />
             <param name="organism" value="human" />
             <param name="protein" value="--protein=on" />
             <param name="codingseq" value="--codingseq=on" />
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst	Fri Jun 07 02:30:21 2013 -0400
@@ -0,0 +1,77 @@
+Galaxy wrapper for Augustus
+===========================
+
+This wrapper is copyright 2012-2013 by Björn Grüning.
+
+This is a wrapper for the command line tool of augustus.
+http://bioinf.uni-greifswald.de/augustus/
+
+AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
+
+Oliver Keller, Martin Kollmar, Mario Stanke, Stephan Waack (2011)
+A novel hybrid gene prediction method employing protein multiple sequence alignments
+Bioinformatics, doi: 10.1093/bioinformatics/btr010
+
+Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008)
+Using native and syntenically mapped cDNA alignments to improve de novo gene finding
+Bioinformatics, doi: 10.1093/bioinformatics/btn013
+
+Mario Stanke and Stephan Waack (2003)
+Gene Prediction with a Hidden-Markov Model and a new Intron Submodel. 
+Bioinformatics, Vol. 19, Suppl. 2, pages ii215-ii225
+
+
+Installation
+============
+
+The recommended installation is by means of the tool shed. If you need to install it manually here is a short introduction.
+
+Install or downlaod augustus from:
+http://bioinf.uni-greifswald.de/augustus/binaries/
+
+and follow the installation instructions or copy the binaries into your $PATH. To install the wrapper copy the augustus folder in the galaxy tools folder and modify the tools_conf.xml file to make the tool available to Galaxy.
+
+For example::
+
+  <section name="Gene Prediction" id="gene_prediction">
+    <tool file="gene_prediction/tools/augustus/augustus.xml" />
+  </section>
+
+
+Set the *AUGUSTUS_CONFIG_PATH* to /path_to_augustus/augustus/config with::
+
+  export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
+
+or modify the wrapper and use the following additional commandline switch::
+
+  --AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
+
+
+History
+=======
+
+- v0.1: Initial public release
+- v0.2: Added tool_dependencies.xml file and update the augustus version (thanks to James Johnson)
+- v0.3: upgrade to augustus 2.7, added new organisms and new parameters, output additional sequence files
+
+Wrapper 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.
+
--- a/readme.txt	Thu Jun 06 13:26:37 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,79 +0,0 @@
-Galaxy wrapper for Augustus
-=====================================
-
-This wrapper is copyright 2012 by Björn Grüning.
-
-This is a wrapper for the command line tool of augustus.
-http://bioinf.uni-greifswald.de/augustus/
-
-AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
-
-Oliver Keller, Martin Kollmar, Mario Stanke, Stephan Waack (2011)
-A novel hybrid gene prediction method employing protein multiple sequence alignments
-Bioinformatics, doi: 10.1093/bioinformatics/btr010
-
-Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008)
-Using native and syntenically mapped cDNA alignments to improve de novo gene finding
-Bioinformatics, doi: 10.1093/bioinformatics/btn013
-
-Mario Stanke and Stephan Waack (2003)
-Gene Prediction with a Hidden-Markov Model and a new Intron Submodel. 
-Bioinformatics, Vol. 19, Suppl. 2, pages ii215-ii225
-
-
-
-
-Installation
-============
-
-Install or downlaod augustus from:
-
-http://bioinf.uni-greifswald.de/augustus/binaries/
-
-and follow the installation instructions or copy the binaries into your $PATH
-
-To install the wrapper copy the augustus folder in the galaxy tools
-folder and modify the tools_conf.xml file to make the tool available to Galaxy.
-For example:
-
-<section name="Gene Prediction" id="gene_prediction">
-    <tool file="gene_prediction/tools/augustus/augustus.xml" />
-</section>
-
-
-Set the AUGUSTUS_CONFIG_PATH to /path_to_augustus/augustus/config with
-    export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
-or modify the wrapper and use the following additional commandline switch:
-    --AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
-
-
-
-
-History
-=======
-
-v0.1 - Initial public release
-v0.2 - Added tool_dependencies.xml file and update the augustus version (thanks to James Johnson)
-
-
-Wrapper 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.
-