| Previous changeset 9:53af7b5b1b56 (2017-08-21) Next changeset 11:59054f086eca (2018-10-05) |
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Commit message:
Uploaded version 0.36.5 (use conda to resolve tool dependencies) |
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modified:
README.rst trimmomatic.xml |
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removed:
tool_dependencies.xml |
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| diff -r 53af7b5b1b56 -r dfa082f84068 README.rst --- a/README.rst Mon Aug 21 04:59:09 2017 -0400 +++ b/README.rst Mon Mar 05 10:13:48 2018 -0500 |
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| @@ -71,6 +71,8 @@ ========== ====================================================================== Version Changes ---------- ---------------------------------------------------------------------- +0.36.5 - Remove tool_dependencies.xml and always use conda to resolve tool + dependencies 0.36.4 - Add option to provide custom adapter sequences for ILLUMINACLIP - Add options ``minAdapterLength`` and ``keepBothReads`` for ILLUMINACLIP in palindrome mode |
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| diff -r 53af7b5b1b56 -r dfa082f84068 tool_dependencies.xml --- a/tool_dependencies.xml Mon Aug 21 04:59:09 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,27 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="trimmomatic" version="0.36"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip</action> - <action type="move_file" rename_to="trimmomatic.jar"> - <source>trimmomatic-0.36.jar</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="move_directory_files"> - <source_directory>adapters</source_directory> - <destination_directory>$INSTALL_DIR/adapters</destination_directory> - </action> - <action type="set_environment"> - <environment_variable name="TRIMMOMATIC_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable> - </action> - <action type="set_environment"> - <environment_variable name="TRIMMOMATIC_ADAPTERS_PATH" action="set_to">$INSTALL_DIR/adapters</environment_variable> - </action> - </actions> - </install> - <readme>Trimmomatic requires the Java Runtime Environment - </readme> - </package> -</tool_dependency> - |
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| diff -r 53af7b5b1b56 -r dfa082f84068 trimmomatic.xml --- a/trimmomatic.xml Mon Aug 21 04:59:09 2017 -0400 +++ b/trimmomatic.xml Mon Mar 05 10:13:48 2018 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="trimmomatic" name="Trimmomatic" version="0.36.4"> +<tool id="trimmomatic" name="Trimmomatic" version="0.36.5"> <description>flexible read trimming tool for Illumina NGS data</description> <macros> <import>trimmomatic_macros.xml</import> |