# HG changeset patch # User peterjc # Date 1414503696 14400 # Node ID 7cb6523cf4423f124ce0127e824fcb69d7d85324 # Parent 63470b69cc1d4f7a489359a7c38214e05f6573a1 Uploaded v0.0.3, get ps2pdf via dependency on GhostScript package diff -r 63470b69cc1d -r 7cb6523cf442 tools/mummer/README.rst --- a/tools/mummer/README.rst Tue Oct 28 06:56:51 2014 -0400 +++ b/tools/mummer/README.rst Tue Oct 28 09:41:36 2014 -0400 @@ -19,10 +19,9 @@ ====================== This should be straightforward, Galaxy should automatically download and install -the MUMmer files. +the MUMmer files, and GhostScript which provides the ``ps2pdf`` binary. -It also needs the tools ``gnuplot`` and ``ps2pdf`` to be installed and on the -system ``$PATH``. +It also needs the tools ``gnuplot`` to be installed and on the system ``$PATH``. Manual Installation @@ -61,6 +60,7 @@ v0.0.1 - Initial public release. v0.0.2 - Correct typo in Tool identifier. - Include MUMmer citation in Galaxy XML markup. +v0.0.3 - Install ``ps2pdf`` using Tool Shed's GhostScript package. ======= ====================================================================== diff -r 63470b69cc1d -r 7cb6523cf442 tools/mummer/mummer.py --- a/tools/mummer/mummer.py Tue Oct 28 06:56:51 2014 -0400 +++ b/tools/mummer/mummer.py Tue Oct 28 09:41:36 2014 -0400 @@ -25,7 +25,8 @@ stop_err("Error %i from: %s" % (return_code, cmd)) if "-v" in sys.argv [1:]or "--version" in sys.argv[1:]: - print("MUMmer wrapper v0.0.1\n") + print("MUMmer wrapper v0.0.3\n") + # TODO - How to get a version string from the mummer binary? os.system("nucmer --version") os.system("promer --version") os.system("mummerplot --version") diff -r 63470b69cc1d -r 7cb6523cf442 tools/mummer/mummer.xml --- a/tools/mummer/mummer.xml Tue Oct 28 06:56:51 2014 -0400 +++ b/tools/mummer/mummer.xml Tue Oct 28 09:41:36 2014 -0400 @@ -1,8 +1,13 @@ - + Combine mummer/nucmer/promer with mummerplot + ps2pdf + ghostscript + + mummer nucmer + promer mummerplot mummer diff -r 63470b69cc1d -r 7cb6523cf442 tools/mummer/tool_dependencies.xml --- a/tools/mummer/tool_dependencies.xml Tue Oct 28 06:56:51 2014 -0400 +++ b/tools/mummer/tool_dependencies.xml Tue Oct 28 09:41:36 2014 -0400 @@ -3,4 +3,7 @@ + + +