Re: [galaxy-dev] PATH set in tool env.sh leaking through to set_metadata.py
On 21.01.2015 16:11, John Chilton wrote: So the tool dependency stuff didn't change - but the local job runner now behaves like the other job runners (DRMAA, PBS, etc...) so you have uncovered a bug for all of them I think. Is this a tool shed tool or a locally created dependency? This is a tool shed tool (package_mimodd_0_1_5), but one I uploaded myself (I discovered the bug when I did a test install after updating our local Galaxy). I need to think about how to solve this more generally but if you want a quick work around - I think it would work to just replace python in $GALAXY_ROOT/set_metadata.sh with a hard-coded path to Galaxy's python or perhaps just python2. Since I can change the tool shed tool a more global solution could be to simply remove the python symlink from the python3 virtualenv after its created and have the tool use python3 explicitly at runtime. I'll try whether that works, but I think it should. Sorry for the inconvenience and thanks for bringing this to our attention. No problem. I'm glad if I could help with something instead of just asking questions all the time. Wolfgang On Tue, Jan 20, 2015 at 12:52 PM, John Chilton jmchil...@gmail.com wrote: Are you using the local job runner (this will be the case if you haven't explicitly configured something like pbs or DRMAA in your job_conf.xml file)? -John On Tue, Jan 20, 2015 at 12:34 PM, Wolfgang Maier wolfgang.ma...@biologie.uni-freiburg.de wrote: On 01/20/2015 06:20 PM, Wolfgang Maier wrote: I have not seen this error before (I believe not with latest_2014.10.06) update: confirmed this now. It's enough to hg update to latest_2014.10.06 and things are working again. The difference is that when building the dependency shell command the latest release seems to put the call to set_metadata.sh into that command, while before it seems it was run separately. Wolfgang ___ 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/
Re: [galaxy-dev] PATH set in tool env.sh leaking through to set_metadata.py
Hi, Could this be related to the fact that galaxy is not seeing the tools that are installed in /usr/local/bin?? I'm on latest_2015.01.13 and since the two last upgrades I saw that interproscan and bsmap were not found by galaxy. Both are installed in /usr/local and when invoked on the command line, as the galaxy user, they work perfectly well. Before the last two upgrades both worked from within galaxy. Cristian Date: Wed, 21 Jan 2015 10:11:43 -0500 From: jmchil...@gmail.com To: wolfgang.ma...@biologie.uni-freiburg.de CC: galaxy-...@lists.bx.psu.edu Subject: Re: [galaxy-dev] PATH set in tool env.sh leaking through to set_metadata.py So the tool dependency stuff didn't change - but the local job runner now behaves like the other job runners (DRMAA, PBS, etc...) so you have uncovered a bug for all of them I think. Is this a tool shed tool or a locally created dependency? I need to think about how to solve this more generally but if you want a quick work around - I think it would work to just replace python in $GALAXY_ROOT/set_metadata.sh with a hard-coded path to Galaxy's python or perhaps just python2. Sorry for the inconvenience and thanks for bringing this to our attention. -John On Tue, Jan 20, 2015 at 12:52 PM, John Chilton jmchil...@gmail.com wrote: Are you using the local job runner (this will be the case if you haven't explicitly configured something like pbs or DRMAA in your job_conf.xml file)? -John On Tue, Jan 20, 2015 at 12:34 PM, Wolfgang Maier wolfgang.ma...@biologie.uni-freiburg.de wrote: On 01/20/2015 06:20 PM, Wolfgang Maier wrote: I have not seen this error before (I believe not with latest_2014.10.06) update: confirmed this now. It's enough to hg update to latest_2014.10.06 and things are working again. The difference is that when building the dependency shell command the latest release seems to put the call to set_metadata.sh into that command, while before it seems it was run separately. Wolfgang ___ 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/ ___ 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/
Re: [galaxy-dev] PATH set in tool env.sh leaking through to set_metadata.py
On Wed, Jan 21, 2015 at 6:54 PM, John Chilton jmchil...@gmail.com wrote: On Wed, Jan 21, 2015 at 10:35 AM, Wolfgang Maier wolfgang.ma...@biologie.uni-freiburg.de wrote: On 21.01.2015 16:11, John Chilton wrote: So the tool dependency stuff didn't change - but the local job runner now behaves like the other job runners (DRMAA, PBS, etc...) so you have uncovered a bug for all of them I think. Is this a tool shed tool or a locally created dependency? This is a tool shed tool (package_mimodd_0_1_5), but one I uploaded myself (I discovered the bug when I did a test install after updating our local Galaxy). I need to think about how to solve this more generally but if you want a quick work around - I think it would work to just replace python in $GALAXY_ROOT/set_metadata.sh with a hard-coded path to Galaxy's python or perhaps just python2. Since I can change the tool shed tool a more global solution could be to simply remove the python symlink from the python3 virtualenv after its created and have the tool use python3 explicitly at runtime. I'll try whether that works, but I think it should. This sounds like a better short-term solution to me - this way older versions of Galaxy will still be able to use the recipe. I created a Trello issue to track the longer term fix of isolating metadata generation from the tool environment - which is needed but could be a little disruptive so I would rather push it off until after the next release. Opps - I forgot the link and forgot to cc the mailing list. https://trello.com/c/aMCwYZsN -John Thanks! -John Sorry for the inconvenience and thanks for bringing this to our attention. No problem. I'm glad if I could help with something instead of just asking questions all the time. Wolfgang On Tue, Jan 20, 2015 at 12:52 PM, John Chilton jmchil...@gmail.com wrote: Are you using the local job runner (this will be the case if you haven't explicitly configured something like pbs or DRMAA in your job_conf.xml file)? -John On Tue, Jan 20, 2015 at 12:34 PM, Wolfgang Maier wolfgang.ma...@biologie.uni-freiburg.de wrote: On 01/20/2015 06:20 PM, Wolfgang Maier wrote: I have not seen this error before (I believe not with latest_2014.10.06) update: confirmed this now. It's enough to hg update to latest_2014.10.06 and things are working again. The difference is that when building the dependency shell command the latest release seems to put the call to set_metadata.sh into that command, while before it seems it was run separately. Wolfgang ___ 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/
Re: [galaxy-dev] PATH set in tool env.sh leaking through to set_metadata.py
So the tool dependency stuff didn't change - but the local job runner now behaves like the other job runners (DRMAA, PBS, etc...) so you have uncovered a bug for all of them I think. Is this a tool shed tool or a locally created dependency? I need to think about how to solve this more generally but if you want a quick work around - I think it would work to just replace python in $GALAXY_ROOT/set_metadata.sh with a hard-coded path to Galaxy's python or perhaps just python2. Sorry for the inconvenience and thanks for bringing this to our attention. -John On Tue, Jan 20, 2015 at 12:52 PM, John Chilton jmchil...@gmail.com wrote: Are you using the local job runner (this will be the case if you haven't explicitly configured something like pbs or DRMAA in your job_conf.xml file)? -John On Tue, Jan 20, 2015 at 12:34 PM, Wolfgang Maier wolfgang.ma...@biologie.uni-freiburg.de wrote: On 01/20/2015 06:20 PM, Wolfgang Maier wrote: I have not seen this error before (I believe not with latest_2014.10.06) update: confirmed this now. It's enough to hg update to latest_2014.10.06 and things are working again. The difference is that when building the dependency shell command the latest release seems to put the call to set_metadata.sh into that command, while before it seems it was run separately. Wolfgang ___ 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/
Re: [galaxy-dev] PATH set in tool env.sh leaking through to set_metadata.py
On 01/20/2015 06:20 PM, Wolfgang Maier wrote: I have not seen this error before (I believe not with latest_2014.10.06) update: confirmed this now. It's enough to hg update to latest_2014.10.06 and things are working again. The difference is that when building the dependency shell command the latest release seems to put the call to set_metadata.sh into that command, while before it seems it was run separately. Wolfgang ___ 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/
