Re: [galaxy-dev] Odd error, solution not understood
Ah, thank you very much, Hans-Rudolf. That did the trick. Best regards, Scott On Wed, Sep 14, 2016 at 6:56 AM, Hans-Rudolf Hotz <h...@fmi.ch> wrote: > Hi Scott > > click on the question mark next to 'database' in your history item and set > the "Database/Build" to the genome you need. > > > Regards, Hans-Rudolf > > On 09/13/2016 09:11 PM, Scott Szakonyi wrote: > >> Hi all, >> >> I'm getting the following error when attempting to do a trackster >> visualization: >> >> Error: The requested genome file (/vectorbase/web/Galaxy/galaxy >> /tool-data/shared/ucsc/chrom/?.len) could not be opened. Exiting! >> Couldn't open /vectorbase/web/Galaxy/galaxy/ >> tool-data/shared/ucsc/chrom/?.len >> >> I found a discussion related to this error online at >> https://biostar.usegalaxy.org/p/6938/, but I'm unsure what the offered >> solution actually means in terms of what I need to do. It says " >> You'll need to set your dataset's database/dbkey to your custom >> reference genome before you can visualize it". Can someone point me in >> the right direction to solve this issue? >> >> Thanks in advance, >> >> Scott >> >> -- >> Scott B. Szakonyi >> Research Programmer >> >> *Center for Research Computing* >> 107 Information Technology Center >> Notre Dame, IN 46556 >> http://crc.nd.edu <http://crc.nd.edu/> >> >> >> ___ >> 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/ >> >> -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Odd error, solution not understood
Hi all, I'm getting the following error when attempting to do a trackster visualization: Error: The requested genome file (/vectorbase/web/Galaxy/galaxy/tool-data/shared/ucsc/chrom/?.len) could not be opened. Exiting! Couldn't open /vectorbase/web/Galaxy/galaxy/tool-data/shared/ucsc/chrom/?.len I found a discussion related to this error online at https://biostar.usegalaxy.org/p/6938/, but I'm unsure what the offered solution actually means in terms of what I need to do. It says " You'll need to set your dataset's database/dbkey to your custom reference genome before you can visualize it". Can someone point me in the right direction to solve this issue? Thanks in advance, Scott -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Problem upgrading
Hello, I'm currently running Galaxy 16.01, and I'd like to upgrade to 16.04. However, when I attempt to do so, I get an error, and git log shows I'm still on 16.01. $ sudo git checkout master && pull --ff-only origin master M tool-data/all_fasta.loc.sample Already on 'master' -bash: pull: command not found I also tried updating to the exact version: sudo git checkout v16.04 error: pathspec 'v16.04' did not match any file(s) known to git. For the record, I'm using Git 1.7.1. I took my commands directory from the announcement page at https://docs.galaxyproject.org/en/master/releases/16.04_announce.html Any suggestions for ways to get the 16.04 code are greatly appreciated! Best, -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Error when executing cleanup scripts
Hi Dannon, That absolutely did the trick. Thanks so much for your assistance. Best, Scott On Fri, May 20, 2016 at 9:11 AM, Dannon Baker <dannon.ba...@gmail.com> wrote: > Hi Scott, > > The quick fix is to source your virtualenv first and you should be good to > go. > > -Dannon > > On Fri, May 20, 2016 at 9:07 AM Scott Szakonyi <scott.b.szakony...@nd.edu> > wrote: > >> Hi all, >> >> I'm getting an error when executing the cleanup scripts in Galaxy 16.01. >> It appears the script is unable to import sqlalchemy, but my understanding >> is that Galaxy can't function without it, so I'm at a loss to explain. >> Here's the error I'm getting: >> >> $ sh scripts/cleanup_datasets/delete_userless_histories.sh >> Traceback (most recent call last): >> File "./scripts/cleanup_datasets/cleanup_datasets.py", line 13, in >> >> import sqlalchemy as sa >> ImportError: No module named sqlalchemy >> >> >> We have relatively limited space on our storage server, so it's >> imperative that I be able to execute these scripts and be able to clean up >> deleted material. I welcome any suggestions. >> >> Best regards, >> >> -- >> Scott B. Szakonyi >> Research Programmer >> >> *Center for Research Computing* >> 107 Information Technology Center >> Notre Dame, IN 46556 >> http://crc.nd.edu >> ___ >> 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/ > > -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Error when executing cleanup scripts
Hi all, I'm getting an error when executing the cleanup scripts in Galaxy 16.01. It appears the script is unable to import sqlalchemy, but my understanding is that Galaxy can't function without it, so I'm at a loss to explain. Here's the error I'm getting: $ sh scripts/cleanup_datasets/delete_userless_histories.sh Traceback (most recent call last): File "./scripts/cleanup_datasets/cleanup_datasets.py", line 13, in import sqlalchemy as sa ImportError: No module named sqlalchemy We have relatively limited space on our storage server, so it's imperative that I be able to execute these scripts and be able to clean up deleted material. I welcome any suggestions. Best regards, -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Removing stale references from a history
Hello Hans-Rudolf, I believe there are references to files that no longer exist. The user is in the UK and I'm in the US, so it will take me a bit to investigate the deletion attempt. I'll try to get back to you as soon as possible. Best, Scott On Wed, May 18, 2016 at 3:59 AM, Hans-Rudolf Hotz <h...@fmi.ch> wrote: > Hi Scott > > Can you explain a little bit more what you mean by "file references that > are no longer valid in one of his histories"? > > What happens when your user tries to delete the affected history item? > > > Regards, Hans-Rudolf > > > > > On 05/16/2016 06:21 PM, Scott Szakonyi wrote: > >> Hello, >> >> Due to some problems on our servers, one of our users has file >> references that are no longer valid in one of his histories. He's >> requested that I remove them, but I don't see any particular way to do >> so through the interface. Is there any way to achieve this? I've poked >> around in the database but don't see any obvious link between the >> history and data files. >> >> Thanks in advance, >> >> -- >> Scott B. Szakonyi >> Research Programmer >> >> *Center for Research Computing* >> 107 Information Technology Center >> Notre Dame, IN 46556 >> http://crc.nd.edu <http://crc.nd.edu/> >> >> >> ___ >> 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/ >> >> -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Data manager problem
Hi Will, We did manage to solve that problem by changing the Apache configuration. We added "AllowEncodedSlashes On" to httpd.conf. I'm not sure why the URL encoding changed, only that it did. See if that helps you. Best, Scott On Tue, May 10, 2016 at 8:17 PM, Will Holtz <who...@lygos.com> wrote: > Hi Scott, > > I've recently hit the exact same problem. Have you had any success since > then with resolving this? I did some poking around and made a bit of > progress, but still no solution. > > The Data Manager page under Run Data Manager Tools contains URLs like this: > > > https://galaxy.example.com/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_dbkeys_all_fasta%2Fdata_manager_fetch_genome_all_fasta_dbkey%2F0.0.1 > > Loading that URL results in an attempted load of: > > > https://galaxy.example.com/api/tools/toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_dbkeys_all_fasta%2Fdata_manager_fetch_genome_all_fasta_dbkey%2F0.0.1/build > ? > > Which results in a 404 error. I believe the escaping of the slashes is > accidental, as the they are in the path and not in parameters. Changing the > %2F to / as shown here: > > > https://galaxy.example.com/api/tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.1/build > ? > > results in the URL being found and you get back a bunch of JSON about the > tool. I tried looking in the Galaxy code to see if I could quickly > determine where the /root controller is, but I wasn't successful. Perhaps > this is now enough information that one of the developers might be able to > help us. > > -Will > > On Mon, Apr 11, 2016 at 9:55 AM, Scott Szakonyi <scott.b.szakony...@nd.edu > > wrote: > >> Hello, >> >> I'm having an odd problem after updating to the latest version of Galaxy. >> My users prepare data for analysis using data manager tools, such as >> "data_manager_bwa_mem_index_builder". When an attempt is made to run one of >> these tools, a pop up window opens stating "Tool request failed" and >> underneath "Uncaught error". I've pored over all the Galaxy system logs and >> can't find anything that might indicate what is happening. I've uninstalled >> and reinstalled the data manager tools, restarted both the Galaxy service >> and the server, to no avail. I get this same error with any installed data >> manager, yet all the standard tools are executing correctly and don't seem >> to be having any issues. >> >> If anyone can offer some insight or suggestions for resolving this issue, >> I'd be most appreciative. >> >> Best regards, >> >> -- >> Scott B. Szakonyi >> Research Programmer >> >> *Center for Research Computing* >> 107 Information Technology Center >> Notre Dame, IN 46556 >> http://crc.nd.edu >> >> ___ >> 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/ >> > > > > -- > The information contained in this e-mail message or any attachment(s) may > be confidential and/or privileged and is intended for use only by the > individual(s) to whom this message is addressed. If you are not the > intended recipient, any dissemination, distribution, copying, or use is > strictly prohibited. If you receive this e-mail message in error, please > e-mail the sender at who...@lygos.com and destroy this message and remove > the transmission from all computer directories (including e-mail servers). > > Please consider the environment before printing this email. > -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Question: Cannot start local Galaxy after upgrade to v16.01
Hi Daniel, I'm a relative novice at Galaxy administration, but at first blush it looks like you're missing (or the Galaxy user doesn't have permissions on) the paste process. You can try a GIT status or diff to see if something just didn't download right. Otherwise, check to make sure that your entire galaxy install directory is owned by the Galaxy user and the group that the Galaxy user belongs to. Hope this helps! pkg_resources.DistributionNotFound: Paste -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Issue with GATK in workflow
Hi Greg, That does look quite similar, but the workarounds presented are not solving the issue for us. If you can offer any additional strategies, I would truly appreciate it. Best, Scott On Fri, Apr 15, 2016 at 10:56 AM, Von Kuster, Greg <g...@psu.edu> wrote: > Hi Scott, > > I’m not positive, but this behavior may be related to this issue: > > https://github.com/galaxyproject/galaxy/issues/1881 > > Greg Von Kuster > > On Apr 15, 2016, at 10:52 AM, Scott Szakonyi <scott.b.szakony...@nd.edu > <mailto:scott.b.szakony...@nd.edu>> wrote: > > Hello all, > > We have indexed a genome using the appropriate data manager, for GATK, and > our reference is showing up and working for individual walkers in GATK > 2.8. When designing a workflow, however, the reference genome is not > appearing as an option for many walkers, including indel realigner and > realigner target creator. It is appearing for haplotype caller. Again > outside of the workflow environment the indexed references show up for all > walkers. > > Any thoughts on this issue? > > Thanks! > > -- > Scott B. Szakonyi > Research Programmer > > Center for Research Computing > 107 Information Technology Center > Notre Dame, IN 46556 > http://crc.nd.edu<http://crc.nd.edu/> > ___ > 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/ > > -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Issue with GATK in workflow
Hello all, We have indexed a genome using the appropriate data manager, for GATK, and our reference is showing up and working for individual walkers in GATK 2.8. When designing a workflow, however, the reference genome is not appearing as an option for many walkers, including indel realigner and realigner target creator. It is appearing for haplotype caller. Again outside of the workflow environment the indexed references show up for all walkers. Any thoughts on this issue? Thanks! -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Data manager problem
Hello, I'm having an odd problem after updating to the latest version of Galaxy. My users prepare data for analysis using data manager tools, such as "data_manager_bwa_mem_index_builder". When an attempt is made to run one of these tools, a pop up window opens stating "Tool request failed" and underneath "Uncaught error". I've pored over all the Galaxy system logs and can't find anything that might indicate what is happening. I've uninstalled and reinstalled the data manager tools, restarted both the Galaxy service and the server, to no avail. I get this same error with any installed data manager, yet all the standard tools are executing correctly and don't seem to be having any issues. If anyone can offer some insight or suggestions for resolving this issue, I'd be most appreciative. Best regards, -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Problem with LDAP authentication
Hi all, I'm having some difficulties with logging into my production website. I get the following error message in the logs: galaxy.web.framework.webapp WARNING 2016-04-06 18:47:41,852 User logged in as 'userID' externally, but has a cookie as 'use...@vectorbase.org' invalidating session This started rather suddenly today after there was a space crisis on our hard drive, which is the subject of my other recent email to this list. We are using LDAP for external authentication. The same LDAP server is being used by my "Pre" server, and logins are working fine. I've compared both galaxy.ini and httpd.conf and can't find any discrepancies. If someone has suggestions to offer, I would surely appreciate them. Thanks! -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] File_path setting not working
Hello, I'm trying to set our Galaxy instance to put Dataset and Temporary files on a Symlinked drive, as there isn't sufficient room on the Galaxy server to handle those files. However, I can't get it to work. Even though I've changed these settings, Galaxy still seems to be creating large numbers of files in our local database directory. Am I missing something here? I'm including the relevant section of my galaxy.ini: # -- Files and directories # Dataset files are stored in this directory. #file_path = database/files file_path = /data/galaxy/database/files # Temporary files are stored in this directory. #new_file_path = database/tmp new_file_path = /data/galaxy/tmp Thanks! -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Missing dependency issue
Sorry, I was a bit premature. I did find the INSTALLATION.log file, but it only contains the original error message. I can't seem to find a config.log file anywhere. Thanks! Scott On Fri, Mar 11, 2016 at 8:19 AM, Scott Szakonyi <scott.b.szakony...@nd.edu> wrote: > Hello Peter, > > Sadly, when I look in '../Galaxy/shed_tools/ > toolshed.g2.bx.psu.edu/repos/iuc/package_readline_6_2/52d6f646b3b5/package_readline_6_2' > I don't see an installation log anywhere in the tree. I don't know what is > going on... I've always installed via the toolshed, so I don't think I've > done anything to mess it up through manual installations or so forth. I'll > keep looking, but if you or other folks on the list have additional > suggestions I would welcome them. > > Best, > > Scott > > On Thu, Mar 10, 2016 at 7:28 AM, Peter Briggs < > peter.bri...@manchester.ac.uk> wrote: > >> Hello Scott >> >> I don't have any insight into your specific problem with the readline >> package, however it might be worth looking for the INSTALLATION.log file >> from the tool install process. >> >> Assuming that this is the iuc version of package_readline_6_2 then you >> can try looking for it under >> >> >> .../tool_dependencies/readline/6.2/iuc/package_readline_6_2/52d6f646b3b5/ >> >> (the final subdirectory corresponds to the version hash so might be >> different for your installation). >> >> If present the INSTALLATION.log file should be in there and hopefully >> will give you some clues as to what the problem could be. >> >> HTH >> >> Best wishes >> >> Peter >> >> On 09/03/16 20:33, Scott Szakonyi wrote: >> >>> Hello all, >>> >>> I'm having an issue with a missing dependency for readline 6.2. When I >>> try to install or repair, I get the following error message: >>> >>> configure: error: in >>> `/vectorbase/web/Galaxy/galaxy/data/galaxy/tmp/tmp-toolshed-mtd3fhemK/readline-6.2': >>> configure: error: cannot compute suffix of object files: cannot >>> compile >>> See `config.log' for more details. >>> >>> >>> I've tried to locate the config.log file without success, so this is all >>> I have to go on. Has anyone else encountered this sort of issue, and if >>> so, how did you solve it? >>> >>> Thanks! >>> >>> -- >>> Scott B. Szakonyi >>> Research Programmer >>> >>> *Center for Research Computing* >>> 107 Information Technology Center >>> Notre Dame, IN 46556 >>> http://crc.nd.edu <http://crc.nd.edu/> >>> >>> >>> ___ >>> 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/ >>> >>> >> -- >> Peter Briggs peter.bri...@manchester.ac.uk >> Bioinformatics Core Facility University of Manchester >> B.1083 Michael Smith Bldg Tel: (0161) 2751482 >> > > > > -- > Scott B. Szakonyi > Research Programmer > > *Center for Research Computing* > 107 Information Technology Center > Notre Dame, IN 46556 > http://crc.nd.edu > -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Missing dependency issue
Hello Peter, Sadly, when I look in '../Galaxy/shed_tools/ toolshed.g2.bx.psu.edu/repos/iuc/package_readline_6_2/52d6f646b3b5/package_readline_6_2' I don't see an installation log anywhere in the tree. I don't know what is going on... I've always installed via the toolshed, so I don't think I've done anything to mess it up through manual installations or so forth. I'll keep looking, but if you or other folks on the list have additional suggestions I would welcome them. Best, Scott On Thu, Mar 10, 2016 at 7:28 AM, Peter Briggs <peter.bri...@manchester.ac.uk > wrote: > Hello Scott > > I don't have any insight into your specific problem with the readline > package, however it might be worth looking for the INSTALLATION.log file > from the tool install process. > > Assuming that this is the iuc version of package_readline_6_2 then you can > try looking for it under > > > .../tool_dependencies/readline/6.2/iuc/package_readline_6_2/52d6f646b3b5/ > > (the final subdirectory corresponds to the version hash so might be > different for your installation). > > If present the INSTALLATION.log file should be in there and hopefully will > give you some clues as to what the problem could be. > > HTH > > Best wishes > > Peter > > On 09/03/16 20:33, Scott Szakonyi wrote: > >> Hello all, >> >> I'm having an issue with a missing dependency for readline 6.2. When I >> try to install or repair, I get the following error message: >> >> configure: error: in >> `/vectorbase/web/Galaxy/galaxy/data/galaxy/tmp/tmp-toolshed-mtd3fhemK/readline-6.2': >> configure: error: cannot compute suffix of object files: cannot >> compile >> See `config.log' for more details. >> >> >> I've tried to locate the config.log file without success, so this is all >> I have to go on. Has anyone else encountered this sort of issue, and if >> so, how did you solve it? >> >> Thanks! >> >> -- >> Scott B. Szakonyi >> Research Programmer >> >> *Center for Research Computing* >> 107 Information Technology Center >> Notre Dame, IN 46556 >> http://crc.nd.edu <http://crc.nd.edu/> >> >> >> ___ >> 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/ >> >> > -- > Peter Briggs peter.bri...@manchester.ac.uk > Bioinformatics Core Facility University of Manchester > B.1083 Michael Smith Bldg Tel: (0161) 2751482 > -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Missing dependency issue
Hello all, I'm having an issue with a missing dependency for readline 6.2. When I try to install or repair, I get the following error message: configure: error: in `/vectorbase/web/Galaxy/galaxy/data/galaxy/tmp/tmp-toolshed-mtd3fhemK/readline-6.2': configure: error: cannot compute suffix of object files: cannot compile See `config.log' for more details. I've tried to locate the config.log file without success, so this is all I have to go on. Has anyone else encountered this sort of issue, and if so, how did you solve it? Thanks! -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Fwd: Galaxy Conference
Hi Martin, Thank you for the quick response! However, I'm unclear... is "Training Day One" different from the mix of individual session listed there, or does training day one consist of those other sessions that I sign up for? I have created a sched account, I'm just a bit confused about the relationship of things. Thanks! Scott On Fri, Mar 4, 2016 at 11:35 AM, Martin Čech <mar...@bx.psu.edu> wrote: > Hello Scott, > > have you seen the schedule at https://gcc16.sched.org/ ? > > The trainings are all listed, described, and categorized there, it should > help you decide what to attend. > From my experience in addition to scientists there are many admins and > developers attending the conference so you should be able to find your > flock easily. > > Plus we are all nice. :) > > Best, > Martin > > On Fri, Mar 4, 2016 at 11:32 AM Scott Szakonyi <scott.b.szakony...@nd.edu> > wrote: > >> Hi all, >> >> I know this is not a technical question per se, but this seems my best >> option for getting better information. >> >> I am planning on attending the Galaxy Conference this year. I >> administrate the Galaxy server for VectorBase (vectorbase.org), but I'm >> a computer scientist, not a bioinformatics specialist. I'm uncertain what >> would be the most informative things for me to attend... for instance, I >> see there is a training day 1 and 2, but there's no real description on the >> site of what those are. If someone could offer some guidance, I would be >> most appreciative. >> >> Also, would the conference days be useful for someone in my position? >> >> Thanks! >> >> -- >> Scott B. Szakonyi >> Research Programmer >> >> *Center for Research Computing* >> 107 Information Technology Center >> Notre Dame, IN 46556 >> http://crc.nd.edu >> ___ >> 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/ > > -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Galaxy Conference
Hi all, I know this is not a technical question per se, but this seems my best option for getting better information. I am planning on attending the Galaxy Conference this year. I administrate the Galaxy server for VectorBase (vectorbase.org), but I'm a computer scientist, not a bioinformatics specialist. I'm uncertain what would be the most informative things for me to attend... for instance, I see there is a training day 1 and 2, but there's no real description on the site of what those are. If someone could offer some guidance, I would be most appreciative. Also, would the conference days be useful for someone in my position? Thanks! -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] GATK problems with data manager
Hi all, Sorry to be repetitive, but this issue is really blocking our efforts to develop the workflow that we need in our instance of Galaxy. If anyone has any familiarity with the issue described below, please let me know. I really need to get this solved. One of my co-administrators is having some issues with data indexed/processed with data managers in GATK. His email to me: Currently there is no way to load a genome into versions of GATK above version 1.4. No version seems to be able to load a reference from history and only version 1.4 seems to work with the available picard-gatk data manager. We need to be able to work with these later versions of GATK, 3.4 on the Galaxy tool shed is the latest. Thanks! Scott -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Difficulty uploading BAM files
Hi Peter, Thanks to you and all the other responders who were so helpful! This did solve my problem right away. Best regards, Scott On Fri, Feb 26, 2016 at 3:13 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > Hi Scott, > > Galaxy itself requires samtools (to deal with BAM files), separately > from any Tool Dependency within the tool calling framework. > > Right now there is no mechanism for datatype definitions to declare a > dependency (e.g. on a binary like samtools, or a Python library). > > Probably samtools should be listed as a requirement on the wiki? > https://wiki.galaxyproject.org/Admin/GetGalaxy > > Peter > > On Fri, Feb 26, 2016 at 5:49 PM, Scott Szakonyi > <scott.b.szakony...@nd.edu> wrote: > > Hi, > > > > I'm having trouble uploading BAM files in our development environment. > Other > > files types are uploading without issue. I'm testing with a small BAM > file I > > downloaded, and I'm able to successfully upload it on our production > server > > and usegalaxy.org. When I try to upload in the development environment, > I > > get the following error: > > > > Traceback (most recent call last): > > File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line > > 431, in > > __main__() > > File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line > > 420, in __main__ > > add_file( dataset, registry, json_file, output_path ) > > File "/vectorbase/web/Galaxy/galaxy/tools/data_source/upload.py", line > > 347, in add_file > > if link_data_only == 'copy_files' and > > datatype.dataset_content_needs_grooming( output_path ): > > File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", > line > > 218, in dataset_content_needs_grooming > > version = self._get_samtools_version() > > File "/vectorbase/web/Galaxy/galaxy/lib/galaxy/datatypes/binary.py", > line > > 179, in _get_samtools_version > > raise Exception(message) > > Exception: Attempting to use functionality requiring samtools, but it > cannot > > be located on Galaxy's PATH. > > > > I've checked my installed tools, and all the same Samtools packages are > > successfully installed on the development environment as in production. I > > don't see any missing dependencies or anything like that. At this point > I'm > > stumped. If anyone can offer some guidance on how to resolve this, I'd be > > most appreciative. > > > > Best regards, > > > > -- > > Scott B. Szakonyi > > Research Programmer > > > > Center for Research Computing > > 107 Information Technology Center > > Notre Dame, IN 46556 > > http://crc.nd.edu > > > > ___ > > 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/ > -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Get data via the cloud?
Hi all, Of course, we need to upload large data files. I understand that the common way to achieve this is with an FTP server, but due to our situation setting one up is problematic. Does Galaxy have any mechanism for retrieving data from cloud resources such as Dropbox, Box, or Google Drive? Thanks in advance, -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Picard tools don't include CreateSequenceDictionary?
Hello all, I have some biologists here at Notre Dame who use the Picard Tools CreateSequenceDictionary application as part of their workflow. I've tried to locate it in the toolshed but all the Picard Tools versions that are available don't seem to include it. Does anyone know where I might find this tool to add to Galaxy? Thanks! -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Picard tools don't include CreateSequenceDictionary?
Hi Nicola, Thank you very much! I'm checking with my biologists to see if any of those tools will work out for us. I'll be sure to open an issue if not. Best, Scott On Mon, Feb 1, 2016 at 10:58 AM, Nicola Soranzo <nsora...@tiscali.it> wrote: > Hi Scott, > it seems that devteam's picard repository in the Tool Shed ( > https://toolshed.g2.bx.psu.edu/view/devteam/picard/ ) does not have a > tool for this, but 4 tools include an automatic conversion of a FASTA > dataset using CreateSequenceDictionary: BedToIntervalList, > MergeBamAlignment, ReorderSam and ValidateSamFile. > > If you think this is not the best approach, please open an issue at > https://github.com/galaxyproject/tools-devteam > > Chees, > Nicola > > > On 01/02/16 14:02, Scott Szakonyi wrote: > > Hello all, > > I have some biologists here at Notre Dame who use the Picard > Tools CreateSequenceDictionary application as part of their workflow. I've > tried to locate it in the toolshed but all the Picard Tools versions that > are available don't seem to include it. Does anyone know where I might find > this tool to add to Galaxy? > > Thanks! > > -- > Scott B. Szakonyi > Research Programmer > > *Center for Research Computing* > 107 Information Technology Center > Notre Dame, IN 46556 > <http://crc.nd.edu/>http://crc.nd.edu > > > ___ > 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/ > > > -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Picard installation dependency issues
Hi Martin, I've been able to resolve all of the issues with Picard dependencies except for Cairo. It's still failing with this error: Tool shed repository:package_cairo_1_12_14 Tool shed repository changeset revision:f5ab0fdf3716 Tool dependency status:Error Tool dependency installation error:/bin/sh: -c: line 14: syntax error: unexpected end of file If you have any suggestions about this error, I'd be pleased to attempt to resolve it. Best, Scott On Tue, Dec 1, 2015 at 10:01 AM, Scott Szakonyi <scott.b.szakony...@nd.edu> wrote: > Hi Martin, > > Thanks very much for your reply, and also to Marius. > > After some investigation, it appears that there is a firewall issue on my > Galaxy server which is preventing the download of the file via FTP. I'm > looking into options for that now. > > Best, > > Scott > > On Tue, Dec 1, 2015 at 9:56 AM, Martin Čech <mar...@bx.psu.edu> wrote: > >> Hello Scott, >> >> thanks to Marius van den Beek the first two issues should be fixed with >> this PR: https://github.com/galaxyproject/tools-devteam/pull/299 >> >> These changes were already propagated to the Main Tool Shed. >> Note for tool developers: for future endeavours please use packages from >> the IUC repository ( >> https://github.com/galaxyproject/tools-iuc/tree/master/packages) >> >> As of the timeout for the readline package it seems the problem was on >> the ftp.gnu side and it is now resolved. >> In the future Galaxy plans to use a smart caching proxy to handle >> all source codes required by the Tool Shed installations. This effort is >> lead by Eric Rasche and you can see it here >> https://github.com/galaxyproject/cargo-port >> >> Thank you for the report (and for using Galaxy :)). >> >> Martin >> >> On Mon, Nov 30, 2015 at 11:29 AM Scott Szakonyi < >> scott.b.szakony...@nd.edu> wrote: >> >>> Hi all, >>> >>> I'm installing the latest revision of Picard tools (efc56ee1ade4). >>> Picard installs successfully, and the tools are appearing in the >>> appropriate menu, but several packages that install with Picard are >>> reporting dependency issues, and I'm concerned that not all the tools will >>> work appropriately. The tools reporting issues are: >>> >>>- package_cairo_1_12_14 (last lines of long warning/error sequence) >>>- >>> >>> /vectorbase/web/Galaxy/galaxy-dist/dependency_dir/libpng/1.6.7/devteam/package_libpng_1_6_7/f48b920cae1f/lib: >>> file not recognized: Is a directory >>> collect2: ld returned 1 exit status >>> make[3]: *** [libcairo.la] Error 1 >>> make[2]: *** [all] Error 2 >>> make[1]: *** [all-recursive] Error 1 >>> make: *** [all] Error 2 >>> - package_pixman_0_32_4 >>>- >>> /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In >>> function `_start': >>> (.text+0x20): undefined reference to `main' >>> collect2: ld returned 1 exit status >>> make[2]: *** [clip-test] Error 1 >>> make[1]: *** [all-recursive] Error 1 >>> make: *** [all] Error 2 >>>- package_readline_6_2 >>>- Error downloading from URL >>> ftp://ftp.gnu.org/gnu/readline/readline-6.2.tar.gz: >>> >>> >>> Is anyone else having issues with these packages? Any suggestions for >>> resolving these problems? >>> >>> Thanks! >>> >>> -- >>> Scott B. Szakonyi >>> Research Programmer >>> >>> *Center for Research Computing* >>> 107 Information Technology Center >>> Notre Dame, IN 46556 >>> http://crc.nd.edu >>> ___ >>> 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/ >> >> > > > -- > Scott B. Szakonyi > Research Programmer > > *Center for Research Computing* > 107 Information Technology Center > Notre Dame, IN 46556 > http://crc.nd.edu > -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Picard installation dependency issues
Excellent! Install completed! Thanks very much. On Tue, Dec 1, 2015 at 3:57 PM, Martin Čech <mar...@bx.psu.edu> wrote: > This is now updated in MTS. Thanks guys. > > M. > > On Tue, Dec 1, 2015 at 4:55 PM Marius van den Beek <m.vandenb...@gmail.com> > wrote: > >> Hi Scott, Martin, >> >> there was still a small problem in cairo. >> I made a PR to fix this ( >> https://github.com/galaxyproject/tools-devteam/pull/300) >> I should have paid a bit more attention ... >> >> Cheers, >> Marius >> >> On 1 December 2015 at 22:46, Scott Szakonyi <scott.b.szakony...@nd.edu> >> wrote: >> >>> Hi Martin, >>> >>> I've been able to resolve all of the issues with Picard dependencies >>> except for Cairo. It's still failing with this error: >>> >>> Tool shed repository:package_cairo_1_12_14 >>> Tool shed repository changeset revision:f5ab0fdf3716 >>> Tool dependency status:Error >>> Tool dependency installation error:/bin/sh: -c: line 14: syntax error: >>> unexpected end of file >>> >>> If you have any suggestions about this error, I'd be pleased to attempt >>> to resolve it. >>> >>> Best, >>> >>> Scott >>> >>> On Tue, Dec 1, 2015 at 10:01 AM, Scott Szakonyi < >>> scott.b.szakony...@nd.edu> wrote: >>> >>>> Hi Martin, >>>> >>>> Thanks very much for your reply, and also to Marius. >>>> >>>> After some investigation, it appears that there is a firewall issue on >>>> my Galaxy server which is preventing the download of the file via FTP. I'm >>>> looking into options for that now. >>>> >>>> Best, >>>> >>>> Scott >>>> >>>> On Tue, Dec 1, 2015 at 9:56 AM, Martin Čech <mar...@bx.psu.edu> wrote: >>>> >>>>> Hello Scott, >>>>> >>>>> thanks to Marius van den Beek the first two issues should be fixed >>>>> with this PR: https://github.com/galaxyproject/tools-devteam/pull/299 >>>>> >>>>> These changes were already propagated to the Main Tool Shed. >>>>> Note for tool developers: for future endeavours please use packages >>>>> from the IUC repository ( >>>>> https://github.com/galaxyproject/tools-iuc/tree/master/packages) >>>>> >>>>> As of the timeout for the readline package it seems the problem was on >>>>> the ftp.gnu side and it is now resolved. >>>>> In the future Galaxy plans to use a smart caching proxy to >>>>> handle all source codes required by the Tool Shed installations. >>>>> This effort is lead by Eric Rasche and you can see it here >>>>> https://github.com/galaxyproject/cargo-port >>>>> >>>>> Thank you for the report (and for using Galaxy :)). >>>>> >>>>> Martin >>>>> >>>>> On Mon, Nov 30, 2015 at 11:29 AM Scott Szakonyi < >>>>> scott.b.szakony...@nd.edu> wrote: >>>>> >>>>>> Hi all, >>>>>> >>>>>> I'm installing the latest revision of Picard tools (efc56ee1ade4). >>>>>> Picard installs successfully, and the tools are appearing in the >>>>>> appropriate menu, but several packages that install with Picard are >>>>>> reporting dependency issues, and I'm concerned that not all the tools >>>>>> will >>>>>> work appropriately. The tools reporting issues are: >>>>>> >>>>>>- package_cairo_1_12_14 (last lines of long warning/error >>>>>>sequence) >>>>>>- >>>>>> >>>>>> /vectorbase/web/Galaxy/galaxy-dist/dependency_dir/libpng/1.6.7/devteam/package_libpng_1_6_7/f48b920cae1f/lib: >>>>>> file not recognized: Is a directory >>>>>> collect2: ld returned 1 exit status >>>>>> make[3]: *** [libcairo.la] Error 1 >>>>>> make[2]: *** [all] Error 2 >>>>>> make[1]: *** [all-recursive] Error 1 >>>>>> make: *** [all] Error 2 >>>>>> - package_pixman_0_32_4 >>>>>>- >>>>>> /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: >>>>>> In function `_start': >>>>>> (.text+0x20): undefined
Re: [galaxy-dev] Picard installation dependency issues
Hi Martin, Thanks very much for your reply, and also to Marius. After some investigation, it appears that there is a firewall issue on my Galaxy server which is preventing the download of the file via FTP. I'm looking into options for that now. Best, Scott On Tue, Dec 1, 2015 at 9:56 AM, Martin Čech <mar...@bx.psu.edu> wrote: > Hello Scott, > > thanks to Marius van den Beek the first two issues should be fixed with > this PR: https://github.com/galaxyproject/tools-devteam/pull/299 > > These changes were already propagated to the Main Tool Shed. > Note for tool developers: for future endeavours please use packages from > the IUC repository ( > https://github.com/galaxyproject/tools-iuc/tree/master/packages) > > As of the timeout for the readline package it seems the problem was on the > ftp.gnu side and it is now resolved. > In the future Galaxy plans to use a smart caching proxy to handle > all source codes required by the Tool Shed installations. This effort is > lead by Eric Rasche and you can see it here > https://github.com/galaxyproject/cargo-port > > Thank you for the report (and for using Galaxy :)). > > Martin > > On Mon, Nov 30, 2015 at 11:29 AM Scott Szakonyi <scott.b.szakony...@nd.edu> > wrote: > >> Hi all, >> >> I'm installing the latest revision of Picard tools (efc56ee1ade4). >> Picard installs successfully, and the tools are appearing in the >> appropriate menu, but several packages that install with Picard are >> reporting dependency issues, and I'm concerned that not all the tools will >> work appropriately. The tools reporting issues are: >> >>- package_cairo_1_12_14 (last lines of long warning/error sequence) >>- >> >> /vectorbase/web/Galaxy/galaxy-dist/dependency_dir/libpng/1.6.7/devteam/package_libpng_1_6_7/f48b920cae1f/lib: >> file not recognized: Is a directory >> collect2: ld returned 1 exit status >> make[3]: *** [libcairo.la] Error 1 >> make[2]: *** [all] Error 2 >> make[1]: *** [all-recursive] Error 1 >> make: *** [all] Error 2 >> - package_pixman_0_32_4 >>- >> /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In >> function `_start': >> (.text+0x20): undefined reference to `main' >> collect2: ld returned 1 exit status >> make[2]: *** [clip-test] Error 1 >> make[1]: *** [all-recursive] Error 1 >> make: *** [all] Error 2 >>- package_readline_6_2 >>- Error downloading from URL >> ftp://ftp.gnu.org/gnu/readline/readline-6.2.tar.gz: >> >> >> Is anyone else having issues with these packages? Any suggestions for >> resolving these problems? >> >> Thanks! >> >> -- >> Scott B. Szakonyi >> Research Programmer >> >> *Center for Research Computing* >> 107 Information Technology Center >> Notre Dame, IN 46556 >> http://crc.nd.edu >> ___ >> 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/ > > -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Error installing tools from toolshed
Nicola, Sorry for the delay... holidays here in the US. That worked perfectly... thank you very much! Best, Scott On Fri, Nov 20, 2015 at 1:59 PM, Nicola Soranzo <nsora...@tiscali.it> wrote: > Hi Scott, > you can try to reinstall it with: "Admin" -> "Manage installed tools", > then click on "Advanced Search" on top, then click on "Deactivated or > uninstalled" and click on "Activate or reinstall" on Trimmomatic menu. > > Cheers, > Nicola > > > On 20/11/15 18:07, Scott Szakonyi wrote: > > Hi Nicola, > > Certainly. On screen, I get a message that says "Revision *f8a9a5eaca8a* of > repository *trimmomatic* owned by *pjbriggs* has already been installed." > > In the logs: > > 129.74.33.163 - - [20/Nov/2015:12:51:44 -0400] "GET > /admin_toolshed/browse_repositories?status=error=Revision+%3Cb%3Ef8a9a5eaca8a%3C%2Fb%3E+of+repository+%3Cb%3Etrimmomatic%3C%2Fb%3E+owned+by+%3Cb%3Epjbriggs%3C%2Fb%3E+has+already+been+installed. > HTTP/1.1" 200 - " > https://galaxy.vectorbase.org:8080/admin_toolshed/browse_repositories; > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_1) AppleWebKit/537.36 (KHTML, > like Gecko) Chrome/46.0.2490.80 Safari/537.36" > 129.74.33.163 - - [20/Nov/2015:12:51:59 -0400] "GET > /admin_toolshed/install_latest_repository_revision?id=d071e794759ab192 > HTTP/1.1" 302 - " > https://galaxy.vectorbase.org:8080/admin_toolshed/browse_repositories?status=error=Revision+%3Cb%3Ef8a9a5eaca8a%3C%2Fb%3E+of+repository+%3Cb%3Etrimmomatic%3C%2Fb%3E+owned+by+%3Cb%3Epjbriggs%3C%2Fb%3E+has+already+been+installed.; > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_1) AppleWebKit/537.36 (KHTML, > like Gecko) Chrome/46.0.2490.80 Safari/537.36" > 129.74.33.163 - - [20/Nov/2015:12:51:59 -0400] "GET > /admin_toolshed/browse_repositories?status=error=Revision+%3Cb%3Ef8a9a5eaca8a%3C%2Fb%3E+of+repository+%3Cb%3Etrimmomatic%3C%2Fb%3E+owned+by+%3Cb%3Epjbriggs%3C%2Fb%3E+has+already+been+installed. > HTTP/1.1" 200 - " > https://galaxy.vectorbase.org:8080/admin_toolshed/browse_repositories?status=error=Revision+%3Cb%3Ef8a9a5eaca8a%3C%2Fb%3E+of+repository+%3Cb%3Etrimmomatic%3C%2Fb%3E+owned+by+%3Cb%3Epjbriggs%3C%2Fb%3E+has+already+been+installed.; > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_1) AppleWebKit/537.36 (KHTML, > like Gecko) Chrome/46.0.2490.80 Safari/537.36" > 129.74.33.163 - - [20/Nov/2015:12:51:59 -0400] "GET > /admin_toolshed/browse_repositories?operation=install+latest+revision=d071e794759ab192 > HTTP/1.1" 302 - " > https://galaxy.vectorbase.org:8080/admin_toolshed/browse_repositories?status=error=Revision+%3Cb%3Ef8a9a5eaca8a%3C%2Fb%3E+of+repository+%3Cb%3Etrimmomatic%3C%2Fb%3E+owned+by+%3Cb%3Epjbriggs%3C%2Fb%3E+has+already+been+installed.; > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_1) AppleWebKit/537.36 (KHTML, > like Gecko) Chrome/46.0.2490.80 Safari/537.36" > > I'm not 100% sure these are in order... I have multiple web handlers > running and the requests get spread out between them. I've tried to order > them as best I can. > > Thanks! > > Scott > > On Fri, Nov 20, 2015 at 12:31 PM, Nicola Soranzo <nsora...@tiscali.it> > wrote: > >> Hi Scott, >> can you try to update Trimmomatic (i.e. go to "Admin" -> "Manage >> installed tools" and click on "Install latest revision" on Trimmomatic >> menu) ? >> If this does not work, copy the relevant log from the Galaxy server and >> post it on the mailing list. >> >> Cheers, >> Nicola >> >> >> On 20/11/15 17:23, Scott Szakonyi wrote: >> >> I was able to switch over to GitHub without issue. Thanks for pointing me >> in the right direction. >> >> I have installed Trimmomatic successfully, although I wasn't able to >> install the latest version. If I try to install the "2015-09-23" revision, >> I get "Internal Server Error Galaxy was unable to successfully complete >> your request". The "2015-04-22" revision installs without issue. >> >> I'm still having troubles with Picard as well, but one thing at a time! >> What information can I provide that might help with getting the latest >> issue of Trimmomatic? >> >> Thanks! >> >> On Fri, Nov 20, 2015 at 9:33 AM, Nicola Soranzo < <nsora...@tiscali.it> >> nsora...@tiscali.it> wrote: >> >>> Hi Scott, >>> the mercurial mirror is not up to date unfortunately, see this previous >>> discussion: >>> >>> >>> http://dev.list.galaxyproject.org/Bismark-installation-dependencies-error-td4668186.html >&
Re: [galaxy-dev] Error installing tools from toolshed
I was able to switch over to GitHub without issue. Thanks for pointing me in the right direction. I have installed Trimmomatic successfully, although I wasn't able to install the latest version. If I try to install the "2015-09-23" revision, I get "Internal Server Error Galaxy was unable to successfully complete your request". The "2015-04-22" revision installs without issue. I'm still having troubles with Picard as well, but one thing at a time! What information can I provide that might help with getting the latest issue of Trimmomatic? Thanks! On Fri, Nov 20, 2015 at 9:33 AM, Nicola Soranzo <nsora...@tiscali.it> wrote: > Hi Scott, > the mercurial mirror is not up to date unfortunately, see this previous > discussion: > > > http://dev.list.galaxyproject.org/Bismark-installation-dependencies-error-td4668186.html > > Cheers, > Nicola > > > On 20/11/15 13:13, Scott Szakonyi wrote: > > Hi Nicola, > > I'm not entirely sure which version... but I am still using the mercurial > mirror, which says I'm up to date. Would this be a wise time, then, to > change over to the Git repository directly? > > Thanks! > > Scott > > On Thu, Nov 19, 2015 at 8:15 PM, Nicola Soranzo <nsora...@tiscali.it> > wrote: > >> Hi Scott, >> which Galaxy release are you using? >> This is a bug which should be fixed in an updated release_15.07 git >> branch. >> >> Cheers, >> Nicola >> >> Scott Szakonyi ha scritto >> >> >> Hello all, >> >> I'm having issues installing Trimmomatic and Picard tools from the >> toolshed. The errors are of the following form (Trimmomatic used for the >> example). >> >> Trimmomatic 0.32 package shows an installation error. >> >> Error details: >> >> File >> "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", >> line 142, in install_and_build_package_via_fabric >> >> tool_dependency = self.install_and_build_package( tool_shed_repository, >> tool_dependency, actions_dict ) >> >> File >> "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", >> line 136, in install_and_build_package >> dir = tmp_dir >> File "/usr/lib64/python2.6/contextlib.py", line 34, in __exit__ >> self.gen.throw(type, value, traceback) >> >> File >> "/vectorbase/web/Galaxy/galaxy-dist/eggs/Fabric-1.7.0-py2.6.egg/fabric/context_managers.py", >> line 142, in _setenv >> yield >> >> File >> "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", >> line 100, in install_and_build_package >> initial_download=True ) >> >> File >> "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", >> line 32, in execute_step >> initial_download=initial_download ) >> >> File >> "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", >> line 685, in execute_step >> >> dir = self.url_download( work_dir, downloaded_filename, url, >> extract=True, checksums=checksums ) >> >> File >> "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", >> line 223, in url_download >> extraction_path = archive.extract( install_dir ) >> >> File >> "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", >> line 89, in extract >> os.chmod( absolute_filepath, unix_permissions ) >> >> >> [Errno 2] No such file or directory: >> '/data/galaxy/tmp/tmp-toolshed-mtdeqJvts/Trimmomatic-0.32/Trimmomatic-0.32/' >> >> I've tried several version of the tool with no success. Any thoughts? >> I've searched project website but haven't come up with anything definitive. >> >> Thanks for any help you can offer, >> >> -- >> Scott B. Szakonyi >> Research Programmer >> *Center for Research Computing* >> 107 Information Technology Center >> Notre Dame, IN 46556 >> <http://crc.nd.edu/>http://crc.nd.edu >> >> > > > -- > Scott B. Szakonyi > Research Programmer > > *Center for Research Computing* > 107 Information Technology Center > Notre Dame, IN 46556 > <http://crc.nd.edu/>http://crc.nd.edu > > > -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Visualization issue
Hi all, If I try to build a new track browser from a custom build, I'm not able to see any of the datasets in my build after clicking add datasets and selecting my workflow from history. Am I doing something wrong, or is there a problem? I've been able to recreate this on both my local server and usegalaxy.org. Thanks! -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Error installing tools from toolshed
Hello all, I'm having issues installing Trimmomatic and Picard tools from the toolshed. The errors are of the following form (Trimmomatic used for the example). Trimmomatic 0.32 package shows an installation error. Error details: File "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 142, in install_and_build_package_via_fabric tool_dependency = self.install_and_build_package( tool_shed_repository, tool_dependency, actions_dict ) File "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 136, in install_and_build_package dir = tmp_dir File "/usr/lib64/python2.6/contextlib.py", line 34, in __exit__ self.gen.throw(type, value, traceback) File "/vectorbase/web/Galaxy/galaxy-dist/eggs/Fabric-1.7.0-py2.6.egg/fabric/context_managers.py", line 142, in _setenv yield File "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 100, in install_and_build_package initial_download=True ) File "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 32, in execute_step initial_download=initial_download ) File "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 685, in execute_step dir = self.url_download( work_dir, downloaded_filename, url, extract=True, checksums=checksums ) File "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 223, in url_download extraction_path = archive.extract( install_dir ) File "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 89, in extract os.chmod( absolute_filepath, unix_permissions ) [Errno 2] No such file or directory: '/data/galaxy/tmp/tmp-toolshed-mtdeqJvts/Trimmomatic-0.32/Trimmomatic-0.32/' I've tried several version of the tool with no success. Any thoughts? I've searched project website but haven't come up with anything definitive. Thanks for any help you can offer, -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Security issues
Hello all, In testing our servers for security vulnerabilities, we've detected some cross site scripting and SQL injection problem on our Galaxy server. Is that something that should be reported as a bug/problem? I did search the Trello board but didn't find any open security related items. Thanks! -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Security issues
Thanks Dannon, I will do that. Best, Scott On Tue, Aug 11, 2015 at 10:20 AM, Dannon Baker dannon.ba...@gmail.com wrote: Hi Scott, Serious security problems should not be fixed via pull request - please responsibly disclose these by e-mailing them (with or without patches) to galaxy-...@lists.galaxyproject.org. The Galaxy core development team will issue patches to public servers before announcing the issue to ensure there is time to patch and highlight these fixes widely. We will provide you credit for the discovery when publicly disclosing the issue. -Dannon On Tue, Aug 11, 2015 at 10:16 AM, Scott Szakonyi scott.b.szakony...@nd.edu wrote: Hello all, In testing our servers for security vulnerabilities, we've detected some cross site scripting and SQL injection problem on our Galaxy server. Is that something that should be reported as a bug/problem? I did search the Trello board but didn't find any open security related items. Thanks! -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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/ -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] TopHat error
Hello all, I have a user who is getting the following error when analyzing a FASTQ file using TopHat for Illumina. TopHat v2.0.10 [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [bam_index_core] Invalid BAM header. [bam_index_build2] fail to index the BAM file. Error indexin I've tried reloading the tool and all it's dependencies, to no avail. We've been able to run the same FASTQ file successfully on another Galaxy server with identical tool configuration. I'm out of ideas, being relatively new to Galaxy. Has anyone seen a similar error? Can you offer an possible solutions? Thanks! -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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 server and ssl
Hi Dannon, There are two things I'm seeing, which seem to be independent problems. 1. Https/ssl issue with URLs generated in util.py. It seems the detection of Https is not working properly, therefore the links underlying the toolshed functionality are coming up as http rather than https. The browser then refuses to following them because they are mixed mode. I've gone around this for the moment by hacking the code in util.py, but it's possible (as I'm very new to server administration) that I'm missing some necessary configuration item that I just don't know about. 2. Toolshed installation is not working properly when Galaxy is run with multiple processes. New categories are not created, and the installed tool does not show up in user menus until the Galaxy server is restarted. I've worked around this by running the Galaxy server in single process mode while installing tools. Thanks for the link... I'll look into that and see what I can glean from it. Best regards, Scott On Wed, Feb 18, 2015 at 7:14 PM, Dannon Baker dannon.ba...@gmail.com wrote: Hey Scott, What weird behavior are you seeing? Paste itself isn't going to serve https, though it's definitely possible to configure an upstream proxy to do so. Are you using a setup similar to https://wiki.galaxyproject.org/Admin/Config/nginxProxy#SSL ? -Dannon On Wed Feb 18 2015 at 4:34:51 PM Scott Szakonyi scott.b.szakony...@nd.edu wrote: Hello all, Just curious if anyone has successfully implemented Galaxy with ssl and standalone Paste-based processes. We're attempting to do so, and we're getting some weird behavior, particularly with regards to the Toolshed. Just want to know if it can be done successfully. Thanks! -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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/ -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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] Adding options to a tool
Hello all, I am a new Galaxy admin/developer, so if this is as stupid question please be kind. I am trying to add the ability for a user to choose additional parameters for Tophat for Illumina. After analyzing the Python and XML files in /galaxy-dist/tools/ngs_rna, I came to the conclusion that modifying these files would give me the desired results. However, no changes that I make to these files seem to have any effect whatsoever on the user experience inside the Galaxy server. I can not find any other likely candidates inside galaxy-dist. Am I looking in the wrong place? Is it even possible to add parameters to a tool interface? Thanks in advance for any help you can offer. -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu ___ 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/
