Hi: I just tried to install khmer from the toolshed. I don’t think it’s installing correctly - but I don’t know if it’s a tool problem or something with my setup.
the tool-dep directory has khmer/2.0/crusoe/package_khmer_2_0/c7702a7d26e8/ but it’s empty.
This tool has a package dependency like this:
<?xml version="1.0"?> <tool_dependency> <package name="khmer" version="2.0"> <install version="1.0"> <actions> <action type="setup_python_environment"> <repository changeset_revision="5caf592bb259" name="package_python_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> <package name="python" version="2.7" /> </repository> <package>https://pypi.python.org/packages/source/k/khmer/khmer-2.0.tar.gz#md5=1f610ab...</package> </action> </actions> </install> </package> </tool_dependency>
what does that fragment tag mean? How does this work. Do I have to set up something to deal with making a python environment?
It also uses this @BINARY@ variable that I have not seen before. galaxy search for ‘@BINARY@‘ turns up nothing. Can anybody point me in the right direction here?
Thanks!
Brad
— Brad Langhorst, Ph.D. Development Scientist New England Biolabs
Hi Brad,
can you please try the IUC version of khmer?
Thanks, Bjoern
Am 15.01.2016 um 20:02 schrieb Langhorst, Brad:
Hi: I just tried to install khmer from the toolshed. I don’t think it’s installing correctly - but I don’t know if it’s a tool problem or something with my setup.
the tool-dep directory has khmer/2.0/crusoe/package_khmer_2_0/c7702a7d26e8/ but it’s empty.
This tool has a package dependency like this:
<?xml version="1.0"?>
<tool_dependency> <package name="khmer" version="2.0"> <install version="1.0"> <actions> <action type="setup_python_environment"> <repository changeset_revision="5caf592bb259" name="package_python_2_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> <package name="python" version="2.7" /> </repository> <package>https://pypi.python.org/packages/source/k/khmer/khmer-2.0.tar.gz#md5=1f610abd021254e21b082179a100cd39</package> </action> </actions> </install> </package> </tool_dependency>
what does that fragment tag mean? How does this work. Do I have to set up something to deal with making a python environment?
It also uses this @BINARY@ variable that I have not seen before. galaxy search for ‘@BINARY@‘ turns up nothing. Can anybody point me in the right direction here?
Thanks!
Brad
— Brad Langhorst, Ph.D. Development Scientist New England Biolabs
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Björn,
Should I delete my old repo?
On Fri, Jan 15, 2016 at 10:26 PM Björn Grüning bjoern.gruening@gmail.com wrote:
Hi Brad,
can you please try the IUC version of khmer?
Thanks, Bjoern
Am 15.01.2016 um 20:02 schrieb Langhorst, Brad:
Hi: I just tried to install khmer from the toolshed. I don’t think it’s installing correctly - but I don’t know if it’s a
tool problem or something with my setup.
the tool-dep directory has khmer/2.0/crusoe/package_khmer_2_0/c7702a7d26e8/ but it’s empty.
This tool has a package dependency like this:
<?xml version="1.0"?>
<tool_dependency> <package name="khmer" version="2.0"> <install version="1.0"> <actions> <action type="setup_python_environment"> <repository changeset_revision="5caf592bb259"
name="package_python_2_7" owner="iuc" toolshed=" https://toolshed.g2.bx.psu.edu%22%3E
<package name="python" version="2.7" /> </repository> <package>
https://pypi.python.org/packages/source/k/khmer/khmer-2.0.tar.gz#md5=1f610ab...
</package> > </action> > </actions> > </install> > </package> > </tool_dependency> > > what does that fragment tag mean? > How does this work. > Do I have to set up something to deal with making a python environment? > > It also uses this @BINARY@ variable that I have not seen before. galaxy search for ‘@BINARY@‘ turns up nothing. > Can anybody point me in the right direction here? > > Thanks! > > > > Brad > > — > Brad Langhorst, Ph.D. > Development Scientist > New England Biolabs > > > > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Michael,
can you deprecate it? Than it's not listed in the search.
Would be awesome! Thanks! Bjoern
Am 16.01.2016 um 10:45 schrieb Michael R. Crusoe:
Björn,
Should I delete my old repo?
On Fri, Jan 15, 2016 at 10:26 PM Björn Grüning bjoern.gruening@gmail.com wrote:
Hi Brad,
can you please try the IUC version of khmer?
Thanks, Bjoern
Am 15.01.2016 um 20:02 schrieb Langhorst, Brad:
Hi: I just tried to install khmer from the toolshed. I don’t think it’s installing correctly - but I don’t know if it’s a
tool problem or something with my setup.
the tool-dep directory has khmer/2.0/crusoe/package_khmer_2_0/c7702a7d26e8/ but it’s empty.
This tool has a package dependency like this:
<?xml version="1.0"?>
<tool_dependency> <package name="khmer" version="2.0"> <install version="1.0"> <actions> <action type="setup_python_environment"> <repository changeset_revision="5caf592bb259"
name="package_python_2_7" owner="iuc" toolshed=" https://toolshed.g2.bx.psu.edu%22%3E
<package name="python" version="2.7" /> </repository> <package>
https://pypi.python.org/packages/source/k/khmer/khmer-2.0.tar.gz#md5=1f610ab...
</package> > </action> > </actions> > </install> > </package> > </tool_dependency> > > what does that fragment tag mean? > How does this work. > Do I have to set up something to deal with making a python environment? > > It also uses this @BINARY@ variable that I have not seen before. galaxy search for ‘@BINARY@‘ turns up nothing. > Can anybody point me in the right direction here? > > Thanks! > > > > Brad > > — > Brad Langhorst, Ph.D. > Development Scientist > New England Biolabs > > > > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
galaxy-dev@lists.galaxyproject.org
-
Björn Grüning -
Langhorst, Brad -
Michael R. Crusoe