Mercurial > repos > peterjc > mummer
changeset 2:8f93c1b7609e draft
Uploaded v0.0.3, dependency on GhostScript package to automatically install ps2pdf
| author | peterjc |
|---|---|
| date | Tue, 28 Oct 2014 09:43:52 -0400 |
| parents | b07aa90c95e6 |
| children | 154c000d3fef |
| files | tools/mummer/README.rst tools/mummer/mummer.py tools/mummer/mummer.xml tools/mummer/tool_dependencies.xml |
| diffstat | 4 files changed, 14 insertions(+), 5 deletions(-) [+] |
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--- a/tools/mummer/README.rst Tue Oct 28 06:57:35 2014 -0400 +++ b/tools/mummer/README.rst Tue Oct 28 09:43:52 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 ``$PATH``. +It also needs the tool ``gnuplot`` to be installed and on the system ``$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. ======= ======================================================================
--- a/tools/mummer/mummer.py Tue Oct 28 06:57:35 2014 -0400 +++ b/tools/mummer/mummer.py Tue Oct 28 09:43:52 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")
--- a/tools/mummer/mummer.xml Tue Oct 28 06:57:35 2014 -0400 +++ b/tools/mummer/mummer.xml Tue Oct 28 09:43:52 2014 -0400 @@ -1,8 +1,13 @@ -<tool id="mummerplot_wrapper" name="MUMmer dotplot" version="0.0.2"> +<tool id="mummerplot_wrapper" name="MUMmer dotplot" version="0.0.3"> <description>Combine mummer/nucmer/promer with mummerplot</description> <requirements> + <!-- Needs ps2pdf from ghostscript --> <requirement type="binary">ps2pdf</requirement> + <requirement type="package" version="9.10">ghostscript</requirement> + <!-- Needs mummer, nucmer, promer and mummerplot from MUMmer --> + <requirement type="binary">mummer</requirement> <requirement type="binary">nucmer</requirement> + <requirement type="binary">promer</requirement> <requirement type="binary">mummerplot</requirement> <requirement type="package" version="3.23">mummer</requirement> </requirements>
--- a/tools/mummer/tool_dependencies.xml Tue Oct 28 06:57:35 2014 -0400 +++ b/tools/mummer/tool_dependencies.xml Tue Oct 28 09:43:52 2014 -0400 @@ -3,4 +3,7 @@ <package name="mummer" version="3.23"> <repository changeset_revision="cc6c4d6ebceb" name="package_mummer_3_23" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> + <package name="ghostscript" version="9.10"> + <repository changeset_revision="a285e78179bd" name="package_ghostscript_9_10" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> </tool_dependency>