Mercurial > repos > davidvanzessen > alakazam

changeset 16:3bc1d89fb783 draft default tip

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Uploaded
author davidvanzessen
date Wed, 18 May 2016 04:50:29 -0400
parents 036f0f9aa117
children
files alakazam.xml tool_dependencies.xml
diffstat 2 files changed, 4 insertions(+), 105 deletions(-) [+]
line wrap: on
line diff
--- a/alakazam.xml	Wed May 18 03:39:13 2016 -0400
+++ b/alakazam.xml	Wed May 18 04:50:29 2016 -0400
@@ -1,5 +1,9 @@
 <tool id="alakazam_galaxy" name="buildPhylipLineage " version="1.0">
 	<description>Alakazam</description>
+	<!--<requirements>
+		<requirement type="package" version="0.2.3">alakazam</requirement>
+		<requirement type="package" version="3.2.1">package_r_3_2_1</requirement>
+	</requirements>-->
 	<command interpreter="bash">
 	alakazam.sh $in_file $out_file
 	</command>
@@ -9,10 +13,6 @@
 	<outputs>
 		<data format="tabular" name="out_file" />
 	</outputs>
-	<requirements>
-		<requirement type="package" version="0.2.3">alakazam</requirement>
-		<requirement type="package" version="3.2.1">package_r_3_2_1</requirement>
-	</requirements>
 	<help>		
 
 	</help>
--- a/tool_dependencies.xml	Wed May 18 03:39:13 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,101 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="package_r_3_2_1" version="3.2.1">
-      <repository changeset_revision="77d439695328" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="alakazam" version="0.2.3">
-        <install version="1.0">
-            <actions>
-                <action type="setup_r_environment">
-                    <repository changeset_revision="77d439695328" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="package_r_3_2_1" version="3.2.1" />
-                    </repository>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/BH_1.60.0-2.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/DBI_0.4-1.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/lazyeval_0.1.10.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/magrittr_1.5.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/Rcpp_0.12.5.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/R6_2.1.2.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/assertthat_0.1.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/dplyr_0.4.3.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/ade4_1.7-4.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/seqinr_3.1-3.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/RColorBrewer_1.1-2.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/dichromat_2.0-0.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/plyr_1.8.3.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/colorspace_1.2-6.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/munsell_0.4.3.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/labeling_0.3.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/scales_0.4.0.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/proto_0.3-10.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/stringi_1.0-1.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/stringr_1.0.0.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/reshape2_1.4.1.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/gtable_0.2.0.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/digest_0.6.9.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/ggplot2_2.1.0.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/irlba_2.0.0.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/NMF_0.20.6.tar.gz
-                    </package>
-                    <package>
-                        https://cran.ism.ac.jp/src/contrib/igraph_1.0.1.tar.gz
-                    </package>
-                    <package>
-                        https://bitbucket.org/kleinstein/alakazam/downloads/alakazam_0.2.3.tar.gz
-                    </package>
-                </action>
-            </actions>
-        </install>
-    </package>
-</tool_dependency>