Re: [galaxy-dev] Does anybody know if ts (a task scheduler) is supported under Galaxy.
Hi Shane, please allow me to jump in late - since you are looking for a simple solution: why not rely just on the built in job scheduler? Have a look at ~/config/job_conf.xml.sample_advanced Even on a single box, you can set up different queues with individual restrictions. Hans-Rudolf On 11/24/2015 06:48 PM, Eric Rasche wrote: I'd also recommend HTCondor. Very easy to set up on debian/ubuntu, apt-get has a quick questionnaire that gets you up and running. Cheers, Eric On 11/24/2015 11:46 AM, Björn Grüning wrote: Hi Shane, would Slurm work for you? http://slurm.schedmd.com/ Cheers, Bjoern Am 24.11.2015 um 13:12 schrieb Shane Kelly: Hi, I am looking for a simple task scheduler to use with Galaxy and initially picked Torque, but since my server is a single box, Torque would appear to be overkill? Can I have any input from anyone who may have used it? Thanks for any response ___ 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] tool data_column param issue under workflow mode
Hi If you load a tabular table with type auto there is a possibility that it incorrectly sniffed as a csv file. With type csv the columns are split on commas and not tabs so the data appears in one column. This is especially the case for tab separated files that do not have row names and therefore the same number of tabs in the header row as the next row. Manually change the type to tabular which will solve the problem. One possible solution which add a stricter csv sniff method is in: https://github.com/galaxyproject/galaxy/pull/1156 regards Christian University of Manchester From: Christian Brenninkmeijer Sent: Wednesday, November 25, 2015 9:23 AM To: FGiacomoni INRA Subject: RE: [galaxy-dev] tool data_column param issue under workflow mode Hi If you load a tabular table with type auto there is a possibility that it incorrectly sniffed as a csv file. With type csv the columns are split on commas and not tabs. This is especially the case for tab separated files that do not have row names and therefor the same number of tabs in the header row as the next row. Manually change the type to tabular which will solve the problem. One possible solution which add a stricter csv sniff is in: https://github.com/galaxyproject/galaxy/pull/1156 regards Christian From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of FGiacomoni INRA [franck.giacom...@clermont.inra.fr] Sent: Tuesday, November 24, 2015 2:16 PM To: galaxy-dev@lists.galaxyproject.org Subject: [galaxy-dev] tool data_column param issue under workflow mode Dears, We observed this issue under galaxy release 15.07. Tools with a param tag and type="data_column" in their xml file are impossible to set on a workflow "run" mode. The value of the column stay at "column 1" or void even if your tabular file has more than one column. The setting of the tool is ok in the "analyze data" mode : you can change the value of the column. We tested this issue with home made tools but also with Merge Columns (version 1.0.1) tool - "text manipulation" section on our Galaxy instance. and we detected the issue on the galaxy main instance too... Any idea ? Thanks Marion & Franck ___ 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] tool data_column param issue under workflow mode
Hi! Same problem here but only if my workflow start with an "input type" tool or any other tool, i can not select an option in list for workflow's other tools cf: https://dl.dropboxusercontent.com/u/86878089/Screen%20Shot%202015-11-25%20at%2010.37.26.png definitely not a data type problem ^^' sincerely nils On 25 November 2015 at 10:30, Christian Brenninkmeijer < christian.brenninkmei...@manchester.ac.uk> wrote: > Hi > > If you load a tabular table with type auto there is a possibility that it > incorrectly sniffed as a csv file. With type csv the columns are split on > commas and not tabs so the data appears in one column. > > This is especially the case for tab separated files that do not have row > names and therefore the same number of tabs in the header row as the next > row. > > Manually change the type to tabular which will solve the problem. > > One possible solution which add a stricter csv sniff method is in: > > https://github.com/galaxyproject/galaxy/pull/1156 > > regards > Christian > University of Manchester > -- > *From:* Christian Brenninkmeijer > *Sent:* Wednesday, November 25, 2015 9:23 AM > *To:* FGiacomoni INRA > *Subject:* RE: [galaxy-dev] tool data_column param issue under workflow > mode > > Hi > > If you load a tabular table with type auto there is a possibility that it > incorrectly sniffed as a csv file. With type csv the columns are split on > commas and not tabs. > > This is especially the case for tab separated files that do not have row > names and therefor the same number of tabs in the header row as the next > row. > > Manually change the type to tabular which will solve the problem. > > One possible solution which add a stricter csv sniff is in: > > https://github.com/galaxyproject/galaxy/pull/1156 > > regards > Christian > -- > *From:* galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf > of FGiacomoni INRA [franck.giacom...@clermont.inra.fr] > *Sent:* Tuesday, November 24, 2015 2:16 PM > *To:* galaxy-dev@lists.galaxyproject.org > *Subject:* [galaxy-dev] tool data_column param issue under workflow mode > > Dears, > We observed this issue under galaxy release 15.07. > Tools with a param tag and type="data_column" in their xml file are > impossible to set on a workflow "run" mode. > The value of the column stay at "column 1" or void even if your tabular > file has more than one column. > > The setting of the tool is ok in the "analyze data" mode : you can change > the value of the column. > > We tested this issue with home made tools but also with Merge Columns > (version 1.0.1) tool - "text manipulation" section on our Galaxy instance. > and we detected the issue on the galaxy main instance too... > > Any idea ? > Thanks > Marion & Franck > > ___ > 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] Potential Hackathon proposal: RADSeq
Hi, The doodle is available here: http://doodle.com/poll/hcc83a4yzgnecq4w The issue will be out soon... On Wed, 25 Nov 2015 09:05:23 +0100 mabernard wrote: > Hi, > > 7th and 8th would be great for me. But I agree with Björn, a github > issue to share our ideas and a doodle is a better way to fixe it. > > Have a nice day > > Maria > > Björn Grüning a écrit : > > > Am 24.11.2015 um 20:36 schrieb Tiago Antao: > >> On Tue, 24 Nov 2015 10:38:05 +0100 > >> mabernard wrote: > >> > >>> So I'm in to but not at the date you propose sorry. > >>> Is the possible the week before (between 7th and 11th) or 2 weeks > >>> later (between 29th to 1st)? > >> > >> What about the 7th and 8th (March)? > > > > What about a github issue and a doodle link? > > > >> Is this OK for everybody? > >> > >> Thanks, > >> Tiago > >> ___ > >> 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] Potential Hackathon proposal: RADSeq
Hi, 7th and 8th would be great for me. But I agree with Björn, a github issue to share our ideas and a doodle is a better way to fixe it. Have a nice day Maria Björn Grüning a écrit : Am 24.11.2015 um 20:36 schrieb Tiago Antao: On Tue, 24 Nov 2015 10:38:05 +0100 mabernard wrote: So I'm in to but not at the date you propose sorry. Is the possible the week before (between 7th and 11th) or 2 weeks later (between 29th to 1st)? What about the 7th and 8th (March)? What about a github issue and a doodle link? Is this OK for everybody? Thanks, Tiago ___ 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] Potential Hackathon proposal: RADSeq
Sorry, I answer too quickly. 2 days are a good duration, not too short and easy to schedule. M mabernard a écrit : Hi, 7th and 8th would be great for me. But I agree with Björn, a github issue to share our ideas and a doodle is a better way to fixe it. Have a nice day Maria Björn Grüning a écrit : Am 24.11.2015 um 20:36 schrieb Tiago Antao: On Tue, 24 Nov 2015 10:38:05 +0100 mabernard wrote: So I'm in to but not at the date you propose sorry. Is the possible the week before (between 7th and 11th) or 2 weeks later (between 29th to 1st)? What about the 7th and 8th (March)? What about a github issue and a doodle link? Is this OK for everybody? Thanks, Tiago ___ 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] Does anybody know if ts (a task scheduler) is supported under Galaxy.
Hi Hans-Rudolph, I am grateful to you (and all the other people who share their knowledge on this list) for pointing out a ready made, in-built solution to what I perceived as a problem. Many thanks, Shane >Hi Shane, > > >please allow me to jump in late - since you are looking for a simple >solution: why not rely just on the built in job scheduler? Have a look >at ~/config/job_conf.xml.sample_advanced > >Even on a single box, you can set up different queues with individual >restrictions. > >Hans-Rudolf > > > >On 11/24/2015 06:48 PM, Eric Rasche wrote: >> I'd also recommend HTCondor. >> Very easy to set up on debian/ubuntu, apt-get has a quick >> questionnaire that gets you up and running. >> >> Cheers, >> Eric >> >> On 11/24/2015 11:46 AM, Björn Grüning wrote: >>> Hi Shane, >>> >>> would Slurm work for you? >>> >>> http://slurm.schedmd.com/ >>> >>> Cheers, >>> Bjoern >>> >>> Am 24.11.2015 um 13:12 schrieb Shane Kelly: Hi, I am looking for a simple task scheduler to use with Galaxy and initially picked Torque, but since my server is a single box, Torque would appear to be overkill? Can I have any input from anyone who may have used it? Thanks for any response ___ 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] tool data_column param issue under workflow mode
Thx for reporting this. I am looking into it. On Wed, Nov 25, 2015 at 4:53 AM, Nils Paulhe wrote: > Hi! > > Same problem here but only if my workflow start with an "input type" tool > or any other tool, i can not select an option in list for workflow's other > tools > cf: > https://dl.dropboxusercontent.com/u/86878089/Screen%20Shot%202015-11-25%20at%2010.37.26.png > > definitely not a data type problem ^^' > > sincerely > > nils > > On 25 November 2015 at 10:30, Christian Brenninkmeijer < > christian.brenninkmei...@manchester.ac.uk> wrote: > >> Hi >> >> If you load a tabular table with type auto there is a possibility that it >> incorrectly sniffed as a csv file. With type csv the columns are split on >> commas and not tabs so the data appears in one column. >> >> This is especially the case for tab separated files that do not have row >> names and therefore the same number of tabs in the header row as the next >> row. >> >> Manually change the type to tabular which will solve the problem. >> >> One possible solution which add a stricter csv sniff method is in: >> >> https://github.com/galaxyproject/galaxy/pull/1156 >> >> regards >> Christian >> University of Manchester >> -- >> *From:* Christian Brenninkmeijer >> *Sent:* Wednesday, November 25, 2015 9:23 AM >> *To:* FGiacomoni INRA >> *Subject:* RE: [galaxy-dev] tool data_column param issue under workflow >> mode >> >> Hi >> >> If you load a tabular table with type auto there is a possibility that it >> incorrectly sniffed as a csv file. With type csv the columns are split on >> commas and not tabs. >> >> This is especially the case for tab separated files that do not have row >> names and therefor the same number of tabs in the header row as the next >> row. >> >> Manually change the type to tabular which will solve the problem. >> >> One possible solution which add a stricter csv sniff is in: >> >> https://github.com/galaxyproject/galaxy/pull/1156 >> >> regards >> Christian >> -- >> *From:* galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on >> behalf of FGiacomoni INRA [franck.giacom...@clermont.inra.fr] >> *Sent:* Tuesday, November 24, 2015 2:16 PM >> *To:* galaxy-dev@lists.galaxyproject.org >> *Subject:* [galaxy-dev] tool data_column param issue under workflow mode >> >> Dears, >> We observed this issue under galaxy release 15.07. >> Tools with a param tag and type="data_column" in their xml file are >> impossible to set on a workflow "run" mode. >> The value of the column stay at "column 1" or void even if your tabular >> file has more than one column. >> >> The setting of the tool is ok in the "analyze data" mode : you can change >> the value of the column. >> >> We tested this issue with home made tools but also with Merge Columns >> (version 1.0.1) tool - "text manipulation" section on our Galaxy instance. >> and we detected the issue on the galaxy main instance too... >> >> Any idea ? >> Thanks >> Marion & Franck >> >> ___ >> 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/
