# HG changeset patch # User yhoogstrate # Date 1416405340 18000 # Node ID b2738b4d7c8cda51227c492c234d3c0ad2ea9f96 # Parent 8c4f96e8ebf1d3f141aa0a489e1ccf5b027a2913 Uploaded diff -r 8c4f96e8ebf1 -r b2738b4d7c8c README.md --- a/README.md Thu Nov 13 16:10:47 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,60 +0,0 @@ -EdgeR wrapper for Galaxy -======================== - - - -Implementation of EdgeR supporting quite advanced experimental -designs. - -Development ------------ - -* Repository-Maintainer: Youri Hoogstrate - -* Repository-Development: - -The tool wrapper has been written by Youri Hoogstrate from the Erasmus -Medical Center (Rotterdam, Netherlands) on behalf of the Translational -Research IT (TraIT) project: - - - -More tools by the Translational Research IT (TraIT) project can be found in the following repository: - - - -License -------- - -**R**: - - - -GPL (>=2) - -**BioConductor**: - - - -Artistic License 2.0 - -**EdgeR**: - -GPL (>=2) - -**This wrapper**: - - Copyright (C) 2013-2014 Youri Hoogstrate - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see . diff -r 8c4f96e8ebf1 -r b2738b4d7c8c README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Wed Nov 19 08:55:40 2014 -0500 @@ -0,0 +1,60 @@ +EdgeR wrapper for Galaxy +======================== + + + +Implementation of EdgeR supporting quite advanced experimental +designs. + +Development +----------- + +* Repository-Maintainer: Youri Hoogstrate + +* Repository-Development: + +The tool wrapper has been written by Youri Hoogstrate from the Erasmus +Medical Center (Rotterdam, Netherlands) on behalf of the Translational +Research IT (TraIT) project: + + + +More tools by the Translational Research IT (TraIT) project can be found in the following repository: + + + +License +------- + +**R**: + + + +GPL (>=2) + +**BioConductor**: + + + +Artistic License 2.0 + +**EdgeR**: + +GPL (>=2) + +**This wrapper**: + + Copyright (C) 2013-2014 Youri Hoogstrate + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . diff -r 8c4f96e8ebf1 -r b2738b4d7c8c edgeR_Concatenate_Expression_Matrices.xml --- a/edgeR_Concatenate_Expression_Matrices.xml Thu Nov 13 16:10:47 2014 -0500 +++ b/edgeR_Concatenate_Expression_Matrices.xml Wed Nov 19 08:55:40 2014 -0500 @@ -145,12 +145,16 @@ The tool wrapper has been written by Youri Hoogstrate from the Erasmus Medical Center (Rotterdam, Netherlands) on behalf of the Translational Research IT (TraIT) project: + http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch More tools by the Translational Research IT (TraIT) project can be found in the following toolsheds: -- http://toolshed.dtls.nl/ -- http://toolshed.g2.bx.psu.edu -- http://testtoolshed.g2.bx.psu.edu/ + +http://toolshed.dtls.nl/ + +http://toolshed.g2.bx.psu.edu + +http://testtoolshed.g2.bx.psu.edu/ diff -r 8c4f96e8ebf1 -r b2738b4d7c8c edgeR_Design_from_Expression_Matrix.xml --- a/edgeR_Design_from_Expression_Matrix.xml Thu Nov 13 16:10:47 2014 -0500 +++ b/edgeR_Design_from_Expression_Matrix.xml Wed Nov 19 08:55:40 2014 -0500 @@ -112,12 +112,16 @@ The tool wrapper has been written by Youri Hoogstrate from the Erasmus Medical Center (Rotterdam, Netherlands) on behalf of the Translational Research IT (TraIT) project: + http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch More tools by the Translational Research IT (TraIT) project can be found in the following toolsheds: -- http://toolshed.dtls.nl/ -- http://toolshed.g2.bx.psu.edu -- http://testtoolshed.g2.bx.psu.edu/ + +http://toolshed.dtls.nl/ + +http://toolshed.g2.bx.psu.edu + +http://testtoolshed.g2.bx.psu.edu/ diff -r 8c4f96e8ebf1 -r b2738b4d7c8c edgeR_Differential_Gene_Expression.xml --- a/edgeR_Differential_Gene_Expression.xml Thu Nov 13 16:10:47 2014 -0500 +++ b/edgeR_Differential_Gene_Expression.xml Wed Nov 19 08:55:40 2014 -0500 @@ -608,13 +608,17 @@ The tool wrapper has been written by Youri Hoogstrate from the Erasmus Medical Center (Rotterdam, Netherlands) on behalf of the Translational Research IT (TraIT) project: + http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch More tools by the Translational Research IT (TraIT) project can be found in the following toolsheds: -- http://toolshed.dtls.nl/ -- http://toolshed.g2.bx.psu.edu -- http://testtoolshed.g2.bx.psu.edu/ + +http://toolshed.dtls.nl/ + +http://toolshed.g2.bx.psu.edu + +http://testtoolshed.g2.bx.psu.edu/ I would like to thank Hina Riaz - Naz Khan for her helpful contribution. diff -r 8c4f96e8ebf1 -r b2738b4d7c8c edger_with_design_matrix.tar.xz Binary file edger_with_design_matrix.tar.xz has changed diff -r 8c4f96e8ebf1 -r b2738b4d7c8c tool_dependencies.xml --- a/tool_dependencies.xml Thu Nov 13 16:10:47 2014 -0500 +++ b/tool_dependencies.xml Wed Nov 19 08:55:40 2014 -0500 @@ -1,14 +1,14 @@ - + - + @@ -30,7 +30,7 @@ - + @@ -44,7 +44,8 @@ $INSTALL_DIR/bin/design_matrix_creator - $INSTALL_DIR/bin + $INSTALL_DIR/bin + $REPOSITORY_INSTALL_DIR