[galaxy-dev] Galaxy history UI suggestion
Hello, In the saved histories, the selected page goes to the first page all the times. I think it is not convenient. Let's say I want to browse the histories in page 17. (maybe 20 histories are there). I had to click again the page 17 (button navigation) if I want to browse another history in page 17. It would be great someone can enhance this UI issue (user experience). Thanks! Best, Bongsoo ___ 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] Possible bug in drmaa and Galaxy?
Hi Nicola, Ah! I see! I misunderstood how the logs worked. I thought whatever message Cuffdiff returns with, it passes it to the scheduler. Then, the scheduler in turn passes it to Galaxy. I was confused why Cuffdiff and Galaxy recognized the mistake but the scheduler did not. Now I see! When either reports success or failure, they are actually reporting on two different things. Presumably, this means it's impossible for the scheduler to report an error and Galaxy to report a success? Thanks a lot for taking the time to correct me! I understand now! Ray On Tue, Aug 2, 2016 at 6:12 PM, Nicola Soranzo wrote: > Hi Ray, > I don't see anything strange in the Galaxy logs. The job on the cluster > "finished normally" just means that it completed its execution without being > killed by the cluster scheduler or for other external reasons. The second > line in the logs is telling you that Galaxy has seen that the job returned > an exit code greater than 0, which under Unix means that it terminated with > some error. Therefore Galaxy set the state of the output datasets to Error > and you should see them in red in your history. > > Obviously you may want to fix the cause of the job failure, but it don't > think that this is due to a bug in drmaa or Galaxy itself, probably just the > cufflinks dependency you mentioned. > > Cheers, > Nicola > > > On 02/08/16 10:42, Raymond Wan wrote: >> >> Dear all, >> >> I'm not sure but I think I found a bug somewhere. However, I can't >> tell where the problem is and, so, who to report it to. >> >> This is what I see in paster.log: >> >> - >> galaxy.jobs.runners.drmaa DEBUG 2016-08-01 13:02:08,895 (897/193391) >> state change: job finished normally >> galaxy.jobs.output_checker INFO 2016-08-01 13:02:09,244 Job 897: Fatal >> error: Exit code 1 () >> galaxy.jobs DEBUG 2016-08-01 13:02:09,317 setting dataset state to ERROR >> galaxy.jobs DEBUG 2016-08-01 13:02:09,354 setting dataset state to ERROR >> galaxy.jobs DEBUG 2016-08-01 13:02:09,678 setting dataset state to ERROR >> galaxy.jobs DEBUG 2016-08-01 13:02:09,707 setting dataset state to ERROR >> galaxy.jobs DEBUG 2016-08-01 13:02:09,738 setting dataset state to ERROR >> galaxy.jobs DEBUG 2016-08-01 13:02:09,770 setting dataset state to ERROR >> galaxy.jobs DEBUG 2016-08-01 13:02:09,809 setting dataset state to ERROR >> galaxy.jobs DEBUG 2016-08-01 13:02:09,846 setting dataset state to ERROR >> galaxy.jobs DEBUG 2016-08-01 13:02:09,890 setting dataset state to ERROR >> galaxy.jobs DEBUG 2016-08-01 13:02:09,928 setting dataset state to ERROR >> galaxy.jobs DEBUG 2016-08-01 13:02:09,964 setting dataset state to ERROR >> galaxy.jobs DEBUG 2016-08-01 13:02:10,001 setting dataset state to ERROR >> galaxy.jobs INFO 2016-08-01 13:02:11,560 Collecting metrics for Job 897 >> galaxy.jobs DEBUG 2016-08-01 13:02:11,579 job 897 ended (finish() >> executed in (2402.377 ms)) >> - >> >> As it turns out, there *is* a problem with the run. So, the latter >> error messages are correct. So, I think the first line is wrong. Or >> is this expected behaviour? >> >> About what I'm doing. I'm running the IUC Cuffdiff tool and am using >> it to generate an sqlite database for cummeRbund. It seems that it is >> running the system-installed version of R and some packages are >> missing. (I'm having problems installing the R packages, but I'm >> still investigating this.) >> >> So, there are error messages in the output. Perhaps there is a >> problem with the error message being returned by the tool to the drmaa >> (SLURM, in our case)? >> >> Ray >> ___ >> 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] Galaxy Blast
Cross referencing this open issue which looks like the same thing: https://github.com/peterjc/galaxy_blast/issues/80 We're probably going to return the BLAST datatypes to the Galaxy core, which will resolve this in a different way: https://lists.galaxyproject.org/pipermail/galaxy-dev/2016-August/024696.html https://github.com/galaxyproject/galaxy/pull/2696 Peter On Wed, Jul 27, 2016 at 9:34 AM, Peter Cock wrote: > Thank Dan, that's what I thought. > > So databases can added to any of the multiple blastdb.loc > files which Galaxy ought to be combining. I'm not sure what > went wrong for Harry (and therefore how to avoid it for > others in future). :( > > (Separately I have raised the issue of returning the BLAST > datatypes to the Galaxy core on the IUC mailing list) > > Peter > > On Tue, Jul 26, 2016 at 10:28 PM, Daniel Blankenberg wrote: >> Hi Peter and Harry, >> >> When a tool is installed from the toolshed, the tool data table loc files >> are installed to the configured location and are then referenced in >> shed_tool_data_table_conf.xml. You should be able to modify the .loc files >> as referenced in this file, or, as you did, add a new entry to the >> tool_data_table_conf.xml file. Each instance of the tool data table (one >> will exist per tool shed repository revision that has been installed) will >> be merged together into a single entity that can then be accessed by the >> tools. You can also find the paths to the .loc files for each tool data >> table under the admin interface. Data Managers will write to the specific >> .loc file that was created during their installation. >> >> Please let me know if I can provide additional clarification. >> >> >> >> Thanks for using Galaxy, >> >> Dan >> >> >>> On Jul 26, 2016, at 6:08 AM, Peter Cock wrote: >>> >>> Hello all, >>> >>> Harry (CC'd) emailed me about some teething trouble getting >>> nucleotide BLAST databases to appear in the drop down lists >>> (see below). >>> >>> I suspect this is partly due to the partial data table sample that >>> ships with Galaxy: >>> >>> https://github.com/galaxyproject/galaxy/blob/dev/config/tool_data_table_conf.xml.sample >>> >>> Can any of the Galaxy Data Manager expects advise please? >>> >>> Thanks, >>> >>> Peter >>> >>> >>> -- Forwarded message -- >>> From: Harry Wright >>> Date: Tue, Jul 26, 2016 at 9:25 AM >>> Subject: RE: Galaxy Blast >>> To: Peter Cock >>> >>> >>> Hi Peter, >>> >>> Sorry for the delay in response. If you think it would be useful please >>> post it. >>> >>> I have downloaded what I thought was the newest versions of NCIB >>> blast+ 2.2.31 from the toolshed. >>> >>> The tool_data_table_conf.xml.sample I altered was in galaxy_dir/config/. >>> >>> If you need anything else please ask. >>> >>> Thanks >>> Harry >>> >>> -Original Message- >>> From: Peter Cock [mailto:p.j.a.c...@googlemail.com] >>> Sent: 22 July 2016 16:28 >>> To: Harry Wright >>> Subject: Re: Galaxy Blast >>> >>> Hi Harry, >>> >>> Hmm. I'm a little puzzled. That file looks fine on our GitHub and on >>> the Tool Shed: >>> >>> https://github.com/peterjc/galaxy_blast/blob/master/tool-data/tool_data_table_conf.xml.sample >>> >>> http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus (browse tip >>> files) >>> >>> Can you tell me exactly which version of things you got from the Tool >>> Shed, and exactly which tool_data_table_conf.xml and >>> tool_data_table_conf.xml.sample you had to edit? >>> >>> My guess is the problem is this partial example that ships with Galaxy: >>> >>> https://github.com/galaxyproject/galaxy/blob/dev/config/tool_data_table_conf.xml.sample >>> >>> (There is talk of moving datatypes like this back into the Galaxy >>> core, which would simply this) >>> >>> May I forward this email to the public Galaxy developers mailing list >>> please? >>> >>> Thanks, >>> >>> Peter >>> >>> On Fri, Jul 22, 2016 at 3:59 PM, Harry Wright >>> wrote: Dear Peter, I have just installed a new instance of Galaxy here at Moredun and have been busy setting up tools for us to use. One of the tools that I have set up is blast with the NCBI nr and nt databases sitting in the backend as a Locally installed database. I downloaded both files and formatted them into databases. I then add lines to the blastdb_p.loc and blastdb.loc. When I restarted the server I found that I could access nr through the interface, for blastx, but not nt, using blastn. For nt I was getting the message “No option available” in the Nucleotide BLAST database drop down when I selected “Locally installed BLAST database”. After some searching I found reference to config/tool_data_table_conf.xml.sample. When I look there I could only find reference to blastdb_p and not blastdb. I added the lines below to the file and changed the file name to tool_data_table_conf.xml. I restarted galaxy to find t
Re: [galaxy-dev] Possible bug in drmaa and Galaxy?
Hi Ray, I don't see anything strange in the Galaxy logs. The job on the cluster "finished normally" just means that it completed its execution without being killed by the cluster scheduler or for other external reasons. The second line in the logs is telling you that Galaxy has seen that the job returned an exit code greater than 0, which under Unix means that it terminated with some error. Therefore Galaxy set the state of the output datasets to Error and you should see them in red in your history. Obviously you may want to fix the cause of the job failure, but it don't think that this is due to a bug in drmaa or Galaxy itself, probably just the cufflinks dependency you mentioned. Cheers, Nicola On 02/08/16 10:42, Raymond Wan wrote: Dear all, I'm not sure but I think I found a bug somewhere. However, I can't tell where the problem is and, so, who to report it to. This is what I see in paster.log: - galaxy.jobs.runners.drmaa DEBUG 2016-08-01 13:02:08,895 (897/193391) state change: job finished normally galaxy.jobs.output_checker INFO 2016-08-01 13:02:09,244 Job 897: Fatal error: Exit code 1 () galaxy.jobs DEBUG 2016-08-01 13:02:09,317 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,354 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,678 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,707 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,738 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,770 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,809 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,846 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,890 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,928 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,964 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:10,001 setting dataset state to ERROR galaxy.jobs INFO 2016-08-01 13:02:11,560 Collecting metrics for Job 897 galaxy.jobs DEBUG 2016-08-01 13:02:11,579 job 897 ended (finish() executed in (2402.377 ms)) - As it turns out, there *is* a problem with the run. So, the latter error messages are correct. So, I think the first line is wrong. Or is this expected behaviour? About what I'm doing. I'm running the IUC Cuffdiff tool and am using it to generate an sqlite database for cummeRbund. It seems that it is running the system-installed version of R and some packages are missing. (I'm having problems installing the R packages, but I'm still investigating this.) So, there are error messages in the output. Perhaps there is a problem with the error message being returned by the tool to the drmaa (SLURM, in our case)? Ray ___ 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] Possible bug in drmaa and Galaxy?
Dear all, I'm not sure but I think I found a bug somewhere. However, I can't tell where the problem is and, so, who to report it to. This is what I see in paster.log: - galaxy.jobs.runners.drmaa DEBUG 2016-08-01 13:02:08,895 (897/193391) state change: job finished normally galaxy.jobs.output_checker INFO 2016-08-01 13:02:09,244 Job 897: Fatal error: Exit code 1 () galaxy.jobs DEBUG 2016-08-01 13:02:09,317 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,354 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,678 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,707 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,738 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,770 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,809 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,846 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,890 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,928 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:09,964 setting dataset state to ERROR galaxy.jobs DEBUG 2016-08-01 13:02:10,001 setting dataset state to ERROR galaxy.jobs INFO 2016-08-01 13:02:11,560 Collecting metrics for Job 897 galaxy.jobs DEBUG 2016-08-01 13:02:11,579 job 897 ended (finish() executed in (2402.377 ms)) - As it turns out, there *is* a problem with the run. So, the latter error messages are correct. So, I think the first line is wrong. Or is this expected behaviour? About what I'm doing. I'm running the IUC Cuffdiff tool and am using it to generate an sqlite database for cummeRbund. It seems that it is running the system-installed version of R and some packages are missing. (I'm having problems installing the R packages, but I'm still investigating this.) So, there are error messages in the output. Perhaps there is a problem with the error message being returned by the tool to the drmaa (SLURM, in our case)? Ray ___ 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] Add url in help of tool xml
Great - I'm glad it was an easy fix. Peter On Tue, Aug 2, 2016 at 10:36 AM, Mohamed Kassam wrote: > Hell Peter > The CDATA works perfectly thanks again. > > Mohamed > > 2016-08-02 11:31 GMT+02:00 Peter Cock : >> >> This could be as simple as the & needing to be >> escaped as & or better escaping the whole >> help text using CDATA: >> >> >> https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#help-tag >> >> Can you show us your tool XML file? Is it on GitHub? >> >> Peter >> >> On Tue, Aug 2, 2016 at 10:26 AM, Mohamed Kassam >> wrote: >> > Dear all, >> > >> > I would like to add an url on my help section of a tool on my xml file >> > however it does not work, >> > >> > https://10.38.14.14/api/fs/dir.html?path=/home/user/&user=galaxy >> > >> > I think it is the &user=galaxy doesn't work in the xml . >> > >> > >> > Mohamed >> > >> > ___ >> > 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] Add url in help of tool xml
This could be as simple as the & needing to be escaped as & or better escaping the whole help text using CDATA: https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#help-tag Can you show us your tool XML file? Is it on GitHub? Peter On Tue, Aug 2, 2016 at 10:26 AM, Mohamed Kassam wrote: > Dear all, > > I would like to add an url on my help section of a tool on my xml file > however it does not work, > > https://10.38.14.14/api/fs/dir.html?path=/home/user/&user=galaxy > > I think it is the &user=galaxy doesn't work in the xml . > > > Mohamed > > ___ > 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] Add url in help of tool xml
Dear all, I would like to add an url on my help section of a tool on my xml file however it does not work, https://10.38.14.14/api/fs/dir.html?path=/home/user/&user=galaxy I think it is the &user=galaxy doesn't work in the xml . Mohamed ___ 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/
