changeset 2:ae0b24f726c3 draft default tip

planemo upload for repository https://github.com/goeckslab/multi_fasta_glimmerhmm.git commit 33f2156452e82c882d7cc6a1a69c3c6884eab94a
author sargentl
date Wed, 02 Oct 2019 14:26:29 -0400
parents 6618d16f276c
children
files LICENSE multi_glimmer.py readme.md tool_data_table_conf.xml.sample tool_dependencies.xml
diffstat 2 files changed, 171 insertions(+), 1 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE	Wed Oct 02 14:26:29 2019 -0400
@@ -0,0 +1,170 @@
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--- a/tool_dependencies.xml	Mon May 01 17:44:12 2017 -0400
+++ b/tool_dependencies.xml	Wed Oct 02 14:26:29 2019 -0400
@@ -4,7 +4,7 @@
         <install version="1.0">
             <actions_group>
                 <actions architecture="x86_64" os="linux">
-                    <action type="download_by_url">ftp://ccb.jhu.edu/pub/software/glimmerhmm/GlimmerHMM-3.0.4.tar.gz</action>
+                    <action type="download_by_url">https://ccb.jhu.edu/software/glimmerhmm/dl/GlimmerHMM-3.0.4.tar.gz</action>
                     <action type="move_directory_files">
                         <source_directory>.</source_directory>                       
                         <destination_directory>$INSTALL_DIR</destination_directory>