galaxy-dev August 2016

galaxy-dev@lists.galaxyproject.org

43 participants
72 discussions

Re: [galaxy-dev] tool runner
by Katherine Beaulieu 03 Aug '16

03 Aug '16

On Wed, Aug 3, 2016 at 11:35 AM, Katherine Beaulieu < katherine.beaulieu014(a)gmail.com> wrote: > Generally what I've found is that you have to go to another html page and > in that page's html code you have to specify to go back to galaxy and your > tool wrapper should take care of submitting to the history. Do you have > code on github to look at for this? > > On Wed, Aug 3, 2016 at 11:07 AM, Mohamed Kassam <k.mamoud(a)gmail.com> > wrote: > >> Dear all, >> >> I created a tool in html +pytho, like for the UCSC. My tool is doing a >> process then return a confirmation of the success of the job. >> >> I 'm blocked at the point that I saw that I have to put method="get" but >> how to tell to Galaxy to run the job and submit on my history the process. >> >> Is there any documentation for the html UCSC part. >> >> Best regards, >> >> 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/ >> > >

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Deprecated code file tag
by Katherine Beaulieu 03 Aug '16

03 Aug '16

Hi everyone, I can't remember where I came across this but I read somewhere that the <code file tag is deprecated and I was just wondering if anyone knew what it was being replaced with? I use it to get a list of items from a remote service to display in a select list for two of my tools. Thanks! Katherine

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tool runner
by Mohamed Kassam 03 Aug '16

03 Aug '16

Dear all, I created a tool in html +pytho, like for the UCSC. My tool is doing a process then return a confirmation of the success of the job. I 'm blocked at the point that I saw that I have to put method="get" but how to tell to Galaxy to run the job and submit on my history the process. Is there any documentation for the html UCSC part. Best regards, Mohamed

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Galaxy history UI suggestion
by Bongsoo Park 03 Aug '16

03 Aug '16

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

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Possible bug in drmaa and Galaxy?
by Raymond Wan 02 Aug '16

02 Aug '16

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

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Fwd: Galaxy Blast
by Peter Cock 02 Aug '16

02 Aug '16

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_con… Can any of the Galaxy Data Manager expects advise please? Thanks, Peter ---------- Forwarded message ---------- From: Harry Wright <Harry.Wright(a)moredun.ac.uk> Date: Tue, Jul 26, 2016 at 9:25 AM Subject: RE: Galaxy Blast To: Peter Cock <p.j.a.cock(a)googlemail.com> 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.cock@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_tab… 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_con… (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 <Harry.Wright(a)moredun.ac.uk> 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 that I could now > use nt in blastn. > > > >  > > <table name="blastdb" comment_char="#"> > > <columns>value, name, path</columns> > > <file path="tool-data/blastdb.loc" /> > > </table> > > > > I was wondering if there was something that I have missed or has this > section of the code been missed out of the tool_data_table_conf.xml > file in the installation download? > > > > Regards > > Harry > > > > Dr. Harry Wright > > Moredun Research Institute > > Pentlands Science Park > > Bush Loan > > Penicuik > > Midlothian EH26 0PZ > > Tel - 0131 4455111 > > Fax - 0131 4456235 > > > > The Moredun Research Institute is a limited company registered in Scotland. > Registered number: SC149440 > > The Moredun Research Institute is a charity registered in Scotland. > Registered number: SC022353 > > Registered office: Moredun Research Institute, Pentlands Science Park, > Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK > > The Moredun Research Institute is a limited company registered in Scotland. Registered number: SC149440 The Moredun Research Institute is a charity registered in Scotland. Registered number: SC022353 Registered office: Moredun Research Institue, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK

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Re: [galaxy-dev] Add url in help of tool xml
by Peter Cock 02 Aug '16

02 Aug '16

Great - I'm glad it was an easy fix. Peter On Tue, Aug 2, 2016 at 10:36 AM, Mohamed Kassam <k.mamoud(a)gmail.com> wrote: > Hell Peter > The CDATA works perfectly thanks again. > > Mohamed > > 2016-08-02 11:31 GMT+02:00 Peter Cock <p.j.a.cock(a)googlemail.com>: >> >> 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_x… >> >> Can you show us your tool XML file? Is it on GitHub? >> >> Peter >> >> On Tue, Aug 2, 2016 at 10:26 AM, Mohamed Kassam <k.mamoud(a)gmail.com> >> 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/ > >

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Add url in help of tool xml
by Mohamed Kassam 02 Aug '16

02 Aug '16

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

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Fwd: Returning BLAST datatypes and DB loc files to Galaxy core?
by Peter Cock 01 Aug '16

01 Aug '16

Dear all, I ran this past the IUC first, and the only comments were positive. Although I wasn't at GCC2017 to discuss this in person, I understand that the Galaxy Team now encourages widely used datatypes to be included in the main Galaxy repository, rather than distributed via the Tool Shed. To that end, would a pull request returning the BLAST datatypes and associated database *.loc files be welcome? These are currently on my GitHub repository here: https://github.com/peterjc/galaxy_blast/ And the datatypes are distributed via the Tool Shed here: http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes Assuming this happens, we would need to phase out the tool shed version (but it will still be needed while older Galaxy instances are still running). Are there any pitfalls to worry about if the datatypes are already there with Galaxy and the tool shed version is installed on top? Or the tool shed version was installed but then Galaxy was updated to include the version bundled with Galaxy? Thanks, Peter

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Remote user auth and API
by Sarah DIEHL 01 Aug '16

01 Aug '16

Dear all, since the recent update to 16.04 I get the following error when trying to import a file from a user directory to a data library: AssertionError: use_remote_user is set but HTTP_REMOTE_USER header was not provided I use apache as a proxy and use an LDAP server for authentication. In order to get the API to work previously the apache had to be set to not check authentication for the requests to /api. In the logs I can see that the dataset import is an request to the API, so since the auth is not checked then, there is also no REMOTE_USER header set. What is the recommended way to solve this issue with the current Galaxy version? I disabled the special settings for /api and the dataset import works now. I tried to check the API with an old test script based on bioblend, but I now get the following error: ConnectionError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:645), 0 attempts left: None Previously I could disable it with import requests requests.packages.urllib3.disable_warnings() but that doesn't seem to work anymore (switched to Python 3 now). Since bioblend wraps all the requests methods, I cannot apply any of the common solutions I found online (e.g. set verify=False). Any help to solve these issues is highly appreciated :-). Best regards, Sarah ---- Sarah Diehl HPC System Administrator UNIVERSITÉ DU LUXEMBOURG LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE Campus Belval | Biotech II 6, avenue du Swing L-4371 Belvaux T +352 46 66 44 5360 sarah.diehl(a)uni.lu<mailto:sarah.diehl@uni.lu> http://lcsb.uni.lu<http://lcsb.uni.lu/> ----- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies. -----

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galaxy-dev August 2016