[galaxy-dev] New install and handlers for tools
Galaxy devs, I have just setup a Galaxy instance here in Cardiff University. We have used a VM to host the web frontend and setup DRMAA to connect to our HPC resource. We are still in the process of testing all the functionality it but one aspect which feels a bit strange is how to tell Galaxy to use the web frontend to run the tools which download data. Our HPC resource does not have a connection to the outside world (only the login nodes). I am not sure on the latest version but it seems handlers for tools can only be specified by id not by tool_type or any other class descriptor so non-computational tools can be run elsewhere whilst the computational tasks are run on HPC - I am currently using the id for each tool to specify a destination in the job_conf.xml. Am I missing something obvious? Another aspect I found whilst installing this was the delicate nature of permissions when integrating it with the cluster. This is especially true if ACLs are also used on the filesystem. It seems the versions I installed (a version from November) could fail without much information why it failed in the logs. Also had occasions where Galaxy never found out a job failed even though the log file had an error and traceback (usually when the DRMAA submit failed). Any advice (or documentation) what the disk permissions should be? And if anyone else is using NFS then root_squash on NFS really does cause issues. So after a bit of tweaking and getting used to the structure of the code I got something which seemed to work - I have possible a few fixes which others might find useful mainly to give better feedback in the log. Any advice how best to integrate these back to you - is there a ticketing system to track changes? I must really upgrade Galaxy to a more recent version to see whether these have already been fixed. Many thanks for all the work that goes into Galaxy and look forward collaborating with the community. All the best, Tom -- Thomas GreenSenior Programmer ARCCA, Redwood Building (Tower), King Edward VII Avenue, Cardiff, Wales, CF10 3NB, UK Tel: +44 (0)29 208 79269Fax: +44 (0)29 208 70734 Email: green...@cardiff.ac.ukWeb: http://www.cardiff.ac.uk ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed
On Sat, Feb 15, 2014 at 12:32 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Sat, Feb 15, 2014 at 12:25 PM, Greg Von Kuster g...@bx.psu.edu wrote: On Feb 3, 2014, at 7:01 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Returning to the MIRA4 problem, I got a meaningful test failure which I fixed (I hadn't set an environment variable in the install script), but I now get only partial test output: http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler ... That's all fine, but where are the test results for mira_bait which I would expect to pass? It looks lie the mira_bait tests results are being populated, but the tests are failing, not passing. This doesn't look like an issue with the Tool Shed's install and test framework. Confirmed - the Tool Shed issue where only partial test output was shown is fixed (did you work out why the test output was missing?). I was hoping to see a passing test, but I can now see a failing test (still something not quite right with my dependency installation script - I'll look at this next week hopefully). Hi Greg, I added a little more debug information to the mirabait test, which confirms a problem in the tool_dependencies.xml file: Missing mirabait under $MIRA4, '/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/7fcabeeca5df/mirabait' Folder contained: env.sh i.e. $MIRA4 was set to $INSTALL_DIR which is the folder /ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/7fcabeeca5df/ and (surprisingly) it only contains one file, env.sh Greg: Could you confirm that on the server? i.e. what does this give? $ ls -l /ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/7fcabeeca5df/ ... Upon downloading mira_4.0_linux-gnu_x86_64_static.tar.bz2 and decompressing it, the tool shed should have changed into the main folder mira_4.0_linux-gnu_x86_64_static and then moved the contents of the bin folder into the $INSTALL_DIR, action type=download_by_urlhttps://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0_linux-gnu_x86_64_static.tar.bz2/action action type=move_directory_files source_directorybin/source_directory destination_directory$INSTALL_DIR/destination_directory /action i.e. Move files mira, mirabait, miraconvert and miramem into $INSTALL_DIR I am somewhat puzzled - other tools like the BLAST+ installers use a very similar setup and work fine (although there I used $PATH instead). Thanks, Peter ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] New install and handlers for tools
On Mon, Feb 17, 2014 at 10:26 AM, Thomas Green green...@cardiff.ac.uk wrote: Galaxy devs, ... So after a bit of tweaking and getting used to the structure of the code I got something which seemed to work - I have possible a few fixes which others might find useful mainly to give better feedback in the log. Any advice how best to integrate these back to you - is there a ticketing system to track changes? I must really upgrade Galaxy to a more recent version to see whether these have already been fixed. If you're comfortable with hg and bitbucket, submit a pull request: https://bitbucket.org/galaxy/galaxy-central/pull-requests Galaxy used to use the bitbucket issue tracker but switched to Trello for better project management, see: https://wiki.galaxyproject.org/Issues Peter ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] package_r_xx problem: X11 is not available
Hi all, I installed to package_r_2.11 and r_3x from the devteam to use as tool dependency. All installation goes fine, but when I run my tool I get the following error: Error in png(file = ../Plots/outname.png, bg = white, width = 480, : X11 is not available The tool uses the installed R : /galaxy/galaxy_tool_binaries/R/2.11.0/devteam/package_r_2_11_0/8d0a55bf7aaf/lib/R/bin/R If I force the tool to use the system installed version of R, it works fine. Are there packages available in the toolsheds that allow the 'png' function to work? I already tried the R-packages from boris, but they gave compilation errors... I also tried to install the R-png package from cran as a galaxy dependency, but that didn't help either. Thanks for the help, Geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandewe...@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed
Hi Peter, It looks like you made some changes to your tool dependency recipe since the last test run. Dave B and I followed the latest revision of your recipe and manually installed it using https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0_linux-gnu_x86_64_static.tar.bz2 and it looked ok. Let's see what the restults of tonight's test run is for this repository and if there are still problems after your latest changes we'll track them down. Thanks, Greg Von Kuster On Feb 17, 2014, at 6:15 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Sat, Feb 15, 2014 at 12:32 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Sat, Feb 15, 2014 at 12:25 PM, Greg Von Kuster g...@bx.psu.edu wrote: On Feb 3, 2014, at 7:01 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Returning to the MIRA4 problem, I got a meaningful test failure which I fixed (I hadn't set an environment variable in the install script), but I now get only partial test output: http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler ... That's all fine, but where are the test results for mira_bait which I would expect to pass? It looks lie the mira_bait tests results are being populated, but the tests are failing, not passing. This doesn't look like an issue with the Tool Shed's install and test framework. Confirmed - the Tool Shed issue where only partial test output was shown is fixed (did you work out why the test output was missing?). I was hoping to see a passing test, but I can now see a failing test (still something not quite right with my dependency installation script - I'll look at this next week hopefully). Hi Greg, I added a little more debug information to the mirabait test, which confirms a problem in the tool_dependencies.xml file: Missing mirabait under $MIRA4, '/ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/7fcabeeca5df/mirabait' Folder contained: env.sh i.e. $MIRA4 was set to $INSTALL_DIR which is the folder /ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/7fcabeeca5df/ and (surprisingly) it only contains one file, env.sh Greg: Could you confirm that on the server? i.e. what does this give? $ ls -l /ToolDepsTest/MIRA/4.0/peterjc/mira4_assembler/7fcabeeca5df/ ... Upon downloading mira_4.0_linux-gnu_x86_64_static.tar.bz2 and decompressing it, the tool shed should have changed into the main folder mira_4.0_linux-gnu_x86_64_static and then moved the contents of the bin folder into the $INSTALL_DIR, action type=download_by_urlhttps://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0_linux-gnu_x86_64_static.tar.bz2/action action type=move_directory_files source_directorybin/source_directory destination_directory$INSTALL_DIR/destination_directory /action i.e. Move files mira, mirabait, miraconvert and miramem into $INSTALL_DIR I am somewhat puzzled - other tools like the BLAST+ installers use a very similar setup and work fine (although there I used $PATH instead). Thanks, Peter ___ 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: http://lists.bx.psu.edu/ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed
On Mon, Feb 17, 2014 at 2:57 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Peter, It looks like you made some changes to your tool dependency recipe since the last test run. Yeah, the mira de novo test was missing the test-data input files. But I didn't touch mirabait or the install XML instructions. Dave B and I followed the latest revision of your recipe and manually installed it using https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_4.0_linux-gnu_x86_64_static.tar.bz2 and it looked ok. If you mean you installed it via the Tool Shed, and it worked - that's good :) (Or did you mean manually by running wget, tar, etc, by hand?) Let's see what the restults of tonight's test run is for this repository and if there are still problems after your latest changes we'll track them down. Sure - fingers crossed, Peter ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Reference Genome in snpEff Tool
Howdy! I only see the Caenorhabditis elegans: WS220.64 reference genome listed in the Genome drop down menu in the snpEff tool. If possible, I would like to use the latest human genome hg19. Can it be added as an option? Thanks in advance. Not: I did follow the link to the developer's site, but would prefer to use the tool from within Galaxy. Clint Christensen Research Assistant, Department of Genetics Texas Biomedical Research Institute 7620 NW Loop 410 San Antonio, TX 78245 210-258-9779 cli...@txbiomedgenetics.org ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Setting access role for datasets through the API
Hi, I'm trying to use the API to upload data into galaxy, setting the access and modify roles as I do so. I've managed to get the roles working for the libraries (using LIBRARY_ACCESS_in and LIBRARY_MODIFY_in) but when it's uploaded the access roles for the datasets are all set to my personal role. I had a poke about the form for modifying the permissions of a dataset and took a shot at setting DATATSET_ACCESS_in but with no luck. Is it possible to set the access role for individual datasets using the API? Would this be possible to do at the upload stage or would I need to go over each of the datasets in the library after they've been uploaded and set the access role? Many thanks, Joe Ward (First time posting to anything like this, so please let me know if I've not gone into enough detail etc) ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Local Galaxy web layout
Galaxy developers:I want to change my local Galaxy web layout,for example,delete the top button of Visualization and Cloud or change their positions.Could anyone show me some details about this?Thank you very much. shenw...@gmail.com ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Reference Genome in snpEff Tool
I have the same question. But, I want to use it on Drosophila and use SnpEff for CloudMap pipeline. From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Clint Christensen [cli...@txbiomedgenetics.org] Sent: Monday, February 17, 2014 10:01 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Reference Genome in snpEff Tool Howdy! I only see the Caenorhabditis elegans: WS220.64 reference genome listed in the Genome drop down menu in the snpEff tool. If possible, I would like to use the latest human genome hg19. Can it be added as an option? Thanks in advance. Not: I did follow the link to the developer's site, but would prefer to use the tool from within Galaxy. Clint Christensen Research Assistant, Department of Genetics Texas Biomedical Research Institute 7620 NW Loop 410 San Antonio, TX 78245 210-258-9779 cli...@txbiomedgenetics.org ___ 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: http://lists.bx.psu.edu/ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] FTP password and web interface password
Hello, I set up a FTP server with SFTP support on my galaxy instance. I have a strange behavior when trying to connect by SFTP. Some users cannot authentify (access denied) whereas other can. As all users can login to the web interface with their credentials, I wanted to check if the length of the password could be the problem with SFTP. To do so, I went to the admin interface to reset the password of a user who could connect by SFTP. Then, this user can connect to the galaxy web interface with the new password but not by SFTP ; if we use the old password, it still works for SFTP authenfication as if both passwords are independent. Could you help me to solve the problem? Yec'han Dr. Yec'han LAIZET Ingenieur Bioinformatique Tel: +33 (0)5 57 12 27 75 _ INRA-UMR BIOGECO 1202 Equipe Genetique 69 route d'Arcachon 33612 CESTAS ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Local Galaxy web layout
Hi Shenwiyn Have a look at: ~/galaxy_dist/database/compiled_templates/base_panels.mako.py Regards, Hans-Rudolf On 02/17/2014 08:04 AM, shenw...@gmail.com wrote: Galaxy developers: I want to change my local Galaxy web layout,for example,delete the top button of Visualization and Cloud or change their positions.Could anyone show me some details about this? Thank you very much. shenw...@gmail.com ___ 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: http://lists.bx.psu.edu/ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] FTP password and web interface password
Hi Yec'han, please have a look at https://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP If you are running postgres and you only newly created users can't access the server its probably due to encryption changes. Set use_pbkdf2 = False and reset all passwort for new users. Cheers, Bjoern Am 17.02.2014 17:27, schrieb Yec'han Laizet: Hello, I set up a FTP server with SFTP support on my galaxy instance. I have a strange behavior when trying to connect by SFTP. Some users cannot authentify (access denied) whereas other can. As all users can login to the web interface with their credentials, I wanted to check if the length of the password could be the problem with SFTP. To do so, I went to the admin interface to reset the password of a user who could connect by SFTP. Then, this user can connect to the galaxy web interface with the new password but not by SFTP ; if we use the old password, it still works for SFTP authenfication as if both passwords are independent. Could you help me to solve the problem? Yec'han Dr. Yec'han LAIZET Ingenieur Bioinformatique Tel: +33 (0)5 57 12 27 75 _ INRA-UMR BIOGECO 1202 Equipe Genetique 69 route d'Arcachon 33612 CESTAS ___ 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: http://lists.bx.psu.edu/ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Local Galaxy web layout
Hi Shenwiyn, This has changed recently. Please take a look at: static/scripts/galaxy.menu.js Using that file, you can add/remove/change labels and their position. It is recommended to run pack_scripts.py after changing the source file. Regards, Sam On Mon, Feb 17, 2014 at 11:33 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Shenwiyn Have a look at: ~/galaxy_dist/database/compiled_templates/base_panels.mako.py Regards, Hans-Rudolf On 02/17/2014 08:04 AM, shenw...@gmail.com wrote: Galaxy developers: I want to change my local Galaxy web layout,for example,delete the top button of Visualization and Cloud or change their positions.Could anyone show me some details about this? Thank you very much. shenw...@gmail.com ___ 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: http://lists.bx.psu.edu/ 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: http://lists.bx.psu.edu/ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] space in text tool results in two arguments
Hi Ross,
I did try to use double quotes and curly braces: ${outloc} but it does
not seem to address the issue.
Thanks,
Ketan
On Mon, Feb 17, 2014 at 10:37 PM, Ross ross.laza...@gmail.com wrote:
Hi Ketan.
Please try quotation marks to enclose any parameter containing spaces in
the tool command template - eg something like:
python myscript.py $text_with_spaces $param2 $param3
Please confirm that this solves the problem?
On Tue, Feb 18, 2014 at 12:47 PM, Ketan Maheshwari
ketancmaheshw...@gmail.com wrote:
Hi,
My tool in galaxy accepts text argument which can have zero or more
spaces depending on user requirements. When user inputs one word it is
parsed fine but in the case when user inputs more words separated by space
it results in multiple separate arguments which messes with the way I am
treating commandline args in my script. Is it possible to tell Galaxy to
treat textbox as a single argument irrespective of spaces in the values
provided?
Thanks for any suggestions.
Best,
--
Ketan
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--
Ketan
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Re: [galaxy-dev] space in text tool results in two arguments
Hi Ketan - great news - all the best with your project...
On Tue, Feb 18, 2014 at 3:58 PM, Ketan Maheshwari ke...@mcs.anl.gov wrote:
Ross,
That's correct. It seems I tested on a cached copy of tool. Works now!
Thanks,
Ketan
On Mon, Feb 17, 2014 at 10:55 PM, Ross ross.laza...@gmail.com wrote:
Hi Ketan.
We routinely recommend quotes as you've shown for this reason and it
certainly works for me at least !
Did you reload the tool xml after editing (via the admin menu or via a
galaxy restart) before testing? If not, you tested a cached copy of the
tool!
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=enuser=UCUuEM4J
On Tue, Feb 18, 2014 at 3:40 PM, Ketan Maheshwari
ketancmaheshw...@gmail.com wrote:
Hi Ross,
I did try to use double quotes and curly braces: ${outloc} but it
does not seem to address the issue.
Thanks,
Ketan
On Mon, Feb 17, 2014 at 10:37 PM, Ross ross.laza...@gmail.com wrote:
Hi Ketan.
Please try quotation marks to enclose any parameter containing spaces
in the tool command template - eg something like:
python myscript.py $text_with_spaces $param2 $param3
Please confirm that this solves the problem?
On Tue, Feb 18, 2014 at 12:47 PM, Ketan Maheshwari
ketancmaheshw...@gmail.com wrote:
Hi,
My tool in galaxy accepts text argument which can have zero or more
spaces depending on user requirements. When user inputs one word it is
parsed fine but in the case when user inputs more words separated by space
it results in multiple separate arguments which messes with the way I am
treating commandline args in my script. Is it possible to tell Galaxy to
treat textbox as a single argument irrespective of spaces in the values
provided?
Thanks for any suggestions.
Best,
--
Ketan
___
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and other Galaxy lists, please use the interface at:
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--
Ketan
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Re: [galaxy-dev] Reference Genome in snpEff Tool
Hi Clint, Xiaofei, There are no current plans to include additional genomes to the SnpEff tool on the public Main Galaxy instance at http://usegalaxy.org. The best solution is to either run a local Galaxy (with sufficient resources) or what is probably easier and more practical for many scientific end users, a cloud Galaxy or possibly a Slipstream Appliance. The tool wrapper is in the Tool Shed, so it can be installed and used within your Galaxy, where you can add in any genome that you want that has the appropriate reference data available. Help to get started is in these links: https://wiki.galaxyproject.org/BigPicture/Choices https://wiki.galaxyproject.org/Tool%20Shed Hopefully one of these solutions will work out for both of you! Jen Galaxy team On 2/17/14 8:20 AM, Wang, Xiaofei wrote: I have the same question. But, I want to use it on Drosophila and use SnpEff for CloudMap pipeline. From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Clint Christensen [cli...@txbiomedgenetics.org] Sent: Monday, February 17, 2014 10:01 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Reference Genome in snpEff Tool Howdy! I only see the Caenorhabditis elegans: WS220.64 reference genome listed in the Genome drop down menu in the snpEff tool. If possible, I would like to use the latest human genome hg19. Can it be added as an option? Thanks in advance. Not: I did follow the link to the developer's site, but would prefer to use the tool from within Galaxy. Clint Christensen Research Assistant, Department of Genetics Texas Biomedical Research Institute 7620 NW Loop 410 San Antonio, TX 78245 210-258-9779 cli...@txbiomedgenetics.org ___ 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: http://lists.bx.psu.edu/ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] SnpEff_and_CloudMap_for_other_speices_other_than_worm (galaxy not local)
Hi Xiaofei, I just replied to the other thread about this same question, and left you on the cc. Please check out the cloud option - this is intended to be useful for those that do not want to invest in a local server or manage the associated administrative tasks. If you are working in on a project related to academic research, be aware the Amazon has a grant program that can help with the costs there (Galaxy is free of course!). More details about this are on their web site. http://usegalaxy.org/cloud http://aws.amazon.com/grants/ Good luck with your project! Jen Galaxy team On 2/14/14 9:39 AM, Wang, Xiaofei wrote: Dear, Is it possible to use SnpEff with genomes of other species (e.g. Drosophila) other than C.elegan on galaxy website (not local)? It seems the only option for the genome menu (Caenorhabditis elegants : WS220.64). In fact, I am trying to use CloudMap (the EMS Variant Density Mapping workflow) to analyze data for Drosophila. So, I have to edit the workflow based on my own data. For SnpEff on the workflow, I tried to change Genome to other species from Caenorhabditis elegants : WS. But, there is no other options. Then, I changed it to be set at runtime. When I run the workflow, I still can not change it to other species. Then, I went to see the SnpEff tool on galaxy website and found that there is no other options for Genome option. So, could you help me about this? Could I use SnpEff and CloudMap (the EMS Variant Density Mapping workflow) other than worm? Or, I have to install galaxy locally for this objective? Thank you so much! Have a nice day! ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] FTP password and web interface password
Hi Bjoern, I indeed followed the wiki tutorial to set up my FTP service some time ago. It seems, as you suggest, that newly created users cannot connect by SFTP. I followed the fix by putting the use_pbkdf2 = False line just below the [app:main] and restarted the galaxy server. I have reseted a newly created user password but it still does not work. Yec'han Dr. Yec'han LAIZET Ingenieur Bioinformatique Tel: +33 (0)5 57 12 27 75 _ INRA-UMR BIOGECO 1202 Equipe Genetique 69 route d'Arcachon 33612 CESTAS Le 17/02/2014 18:12, Björn Grüning a écrit : Hi Yec'han, please have a look at https://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP If you are running postgres and you only newly created users can't access the server its probably due to encryption changes. Set use_pbkdf2 = False and reset all passwort for new users. Cheers, Bjoern Am 17.02.2014 17:27, schrieb Yec'han Laizet: Hello, I set up a FTP server with SFTP support on my galaxy instance. I have a strange behavior when trying to connect by SFTP. Some users cannot authentify (access denied) whereas other can. As all users can login to the web interface with their credentials, I wanted to check if the length of the password could be the problem with SFTP. To do so, I went to the admin interface to reset the password of a user who could connect by SFTP. Then, this user can connect to the galaxy web interface with the new password but not by SFTP ; if we use the old password, it still works for SFTP authenfication as if both passwords are independent. Could you help me to solve the problem? Yec'han Dr. Yec'han LAIZET Ingenieur Bioinformatique Tel: +33 (0)5 57 12 27 75 _ INRA-UMR BIOGECO 1202 Equipe Genetique 69 route d'Arcachon 33612 CESTAS ___ 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: http://lists.bx.psu.edu/ 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: http://lists.bx.psu.edu/ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
