Re: [galaxy-dev] file upload
Musa A. Hassan wrote: I am trying to use galaxy for the first time and am running into some early problems. While trying to upload my file which is basically an fq containing illumina short reads, the file won't upload. When I try the fastq extension of the same file, it does but then the file isn't recognized by the galaxy hence it's like I have no file uploaded. Does anyone have an idea what's going on here. I've looked at the short tutorial on galaxy and it seems my file should be fine. Hi Musa, If you're still having troubles uploading these files, could you share the relevant history with me (n...@bx.psu.edu)? Thanks, --nate Musa ___ 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/
Re: [galaxy-dev] Inquiring
Yan Luo wrote: Dear Nate, We have a new issue to use Galaxy. When we login use a general user account, we found: (1) When we upload six fastq files via URL, three of them can be uploaded successfully while the other three can't be uploaded. Hi Yan, Could you expand the history items so it's possible to see what the upload error is? If you set the 'smtp_server' and 'error_email_to' options in the universe_wsgi.ini file, you will also get a new icon in the history item which will allow you to generate a bug report. This bug report will contain the full error message from the upload tool, if the one in the history item is truncated. (2) What's more, even those files can be uploaded, we can't perform the mapping with BWA (NGS: Mapping/Map with BWA) either single end or paired-end. The problem is we can't select which file to do the mapping. The reason the files are not showing up in the tool most likely has to do with file format. The BWA tool expects input files to be in the fastqsanger format. The best way to acheive this is to run your input file through the FASTQ Groomer tool before using it with BWA. (3) If we use an admin account, we can find one file when we perform the mapping and are trying uploading other one to see if we can select from the two files list. (4) Could you please let me know if Galaxy has some restriction for files number, a single file size, or total files size loaded by one user(account)? Galaxy does not have any built-in limitations on file size/count. --nate Please find the attached screenshoots for your reference. Looking forward to hearing from you. Best Wishes, Yan On Tue, Feb 15, 2011 at 9:08 AM, Nate Coraor n...@bx.psu.edu wrote: Yan Luo wrote: Dear Nate, Yes, you are right, for some reason, we couldn't cd to the folder. It is fixed and I restart the Galaxy. The only thing is that it needs about 10 minutes to start. I remembered it is a little fast last week. Is there any problem? Anyway, Galaxy works. Assuming nothing else has changed, it sounds like your NFS server is having some performance problems. --nate Thanks, Yan On Mon, Feb 14, 2011 at 8:49 AM, Nate Coraor n...@bx.psu.edu wrote: Yan Luo wrote: Dear Nate, Thanks for your quick response, I got sever error. and just killed the process. When I ran activate as follows and can't active it: kangtu@dscbc-compute:~$ . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate bash: /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate: Stale NFS file handle kangtu@dscbc-compute:~$ It looks like the NFS mount on which Galaxy lives has gone bad, possibly due to an error with the NFS server. I suggest contacting a local system administrator for assistance. --nate Any suggestion will be appreciate. Best Wishes, Yan On Mon, Feb 14, 2011 at 8:43 AM, Nate Coraor n...@bx.psu.edu wrote: Yan Luo wrote: Dear Nate, I have a new problem, last week, I restarted the Galaxy, but it worked well. This morning, I found I can't start it from browser, but when I check ps auxwww|grep python, I still find it is running, what is problem? What happens when you try to connect via a browser? Is an error message displayed? Connection timeout? kangtu 24468 0.3 0.0 961592 104296 pts/30 Sl+ Feb11 13:43 python ./scripts/paster.py serve universe_wsgi.ini If you reconnect to your screen session and take a look at the output from the Galaxy server, there may be error message displayed which would explain what the problem is. --nate Looking forward to hearing from you. Best Wishes, yan On Fri, Feb 11, 2011 at 11:16 AM, Yan Luo luoma...@gmail.com wrote: Dear Nate, I just used screen, and restarted the galaxy, it works. It is perfect, and I also found that some features can't be used before, when I restart it, everything is fine. Have a wonderful weekend! Best Wishes, Yan ___ 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/
Re: [galaxy-dev] Inquiring
Dear Nate and developers, Could you please let me know if you have any solution for my questions and several attachments sent to you last week? Someone web pages don't work well. Looking forward to hearing from you. Best Wishes, Yan On Mon, Feb 28, 2011 at 4:45 PM, Yan Luo luoma...@gmail.com wrote: Dear Nate, We have a new issue to use Galaxy. When we login use a general user account, we found: (1) When we upload six fastq files via URL, three of them can be uploaded successfully while the other three can't be uploaded. (2) What's more, even those files can be uploaded, we can't perform the mapping with BWA (NGS: Mapping/Map with BWA) either single end or paired-end. The problem is we can't select which file to do the mapping. (3) If we use an admin account, we can find one file when we perform the mapping and are trying uploading other one to see if we can select from the two files list. (4) Could you please let me know if Galaxy has some restriction for files number, a single file size, or total files size loaded by one user(account)? Please find the attached screenshoots for your reference. Looking forward to hearing from you. Best Wishes, Yan On Tue, Feb 15, 2011 at 9:08 AM, Nate Coraor n...@bx.psu.edu wrote: Yan Luo wrote: Dear Nate, Yes, you are right, for some reason, we couldn't cd to the folder. It is fixed and I restart the Galaxy. The only thing is that it needs about 10 minutes to start. I remembered it is a little fast last week. Is there any problem? Anyway, Galaxy works. Assuming nothing else has changed, it sounds like your NFS server is having some performance problems. --nate Thanks, Yan On Mon, Feb 14, 2011 at 8:49 AM, Nate Coraor n...@bx.psu.edu wrote: Yan Luo wrote: Dear Nate, Thanks for your quick response, I got sever error. and just killed the process. When I ran activate as follows and can't active it: kangtu@dscbc-compute:~$ . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate bash: /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate: Stale NFS file handle kangtu@dscbc-compute:~$ It looks like the NFS mount on which Galaxy lives has gone bad, possibly due to an error with the NFS server. I suggest contacting a local system administrator for assistance. --nate Any suggestion will be appreciate. Best Wishes, Yan On Mon, Feb 14, 2011 at 8:43 AM, Nate Coraor n...@bx.psu.edu wrote: Yan Luo wrote: Dear Nate, I have a new problem, last week, I restarted the Galaxy, but it worked well. This morning, I found I can't start it from browser, but when I check ps auxwww|grep python, I still find it is running, what is problem? What happens when you try to connect via a browser? Is an error message displayed? Connection timeout? kangtu 24468 0.3 0.0 961592 104296 pts/30 Sl+ Feb11 13:43 python ./scripts/paster.py serve universe_wsgi.ini If you reconnect to your screen session and take a look at the output from the Galaxy server, there may be error message displayed which would explain what the problem is. --nate Looking forward to hearing from you. Best Wishes, yan On Fri, Feb 11, 2011 at 11:16 AM, Yan Luo luoma...@gmail.com wrote: Dear Nate, I just used screen, and restarted the galaxy, it works. It is perfect, and I also found that some features can't be used before, when I restart it, everything is fine. Have a wonderful weekend! Best Wishes, Yan ___ 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/
Re: [galaxy-dev] possible bug - user log in / browser cache
Ryan Golhar wrote: I have a local instance running. When I'm logged in as user1, log out, then try to log in as user2, I keep getting the You have been logged out message. Its as if the browser's cache is retaining some information. To get around this, after I log out as user1, I have to click on Analyze Data, then click on Log in to log in as user2. I'm running Safari on Mac, but have noticed this with Firefox as well. Hi Ryan, The login page will redirect you back to whatever page you to whatever page you were on before clicking log in. If this page is the logout page, the behavior you reported will be what happens. If you log in from any other page, this should go away. Please let us know if this is not the case. --nate ___ 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/
Re: [galaxy-dev] possible bug - user log in / browser cache
On Mon, Mar 7, 2011 at 5:56 PM, Nate Coraor n...@bx.psu.edu wrote: Ryan Golhar wrote: I have a local instance running. When I'm logged in as user1, log out, then try to log in as user2, I keep getting the You have been logged out message. Its as if the browser's cache is retaining some information. To get around this, after I log out as user1, I have to click on Analyze Data, then click on Log in to log in as user2. I'm running Safari on Mac, but have noticed this with Firefox as well. Hi Ryan, The login page will redirect you back to whatever page you to whatever page you were on before clicking log in. If this page is the logout page, the behavior you reported will be what happens. If you log in from any other page, this should go away. Bug confirmed on Firefox on Mac, and Chrome on Windows using http://test.g2.bx.psu.edu/ I guess you just need to say if the previous page was the logout page, go to the main page instead, rather than a blind redirect. Issue filed: https://bitbucket.org/galaxy/galaxy-central/issue/486 I expect many people to be caught out by this (back when I was debugging a proxy problem I was probably hitting this bug too). Regards, 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/
Re: [galaxy-dev] possible bug - user log in / browser cache
Peter Cock wrote: On Mon, Mar 7, 2011 at 5:56 PM, Nate Coraor n...@bx.psu.edu wrote: Ryan Golhar wrote: I have a local instance running. When I'm logged in as user1, log out, then try to log in as user2, I keep getting the You have been logged out message. Its as if the browser's cache is retaining some information. To get around this, after I log out as user1, I have to click on Analyze Data, then click on Log in to log in as user2. I'm running Safari on Mac, but have noticed this with Firefox as well. Hi Ryan, The login page will redirect you back to whatever page you to whatever page you were on before clicking log in. If this page is the logout page, the behavior you reported will be what happens. If you log in from any other page, this should go away. Bug confirmed on Firefox on Mac, and Chrome on Windows using http://test.g2.bx.psu.edu/ I guess you just need to say if the previous page was the logout page, go to the main page instead, rather than a blind redirect. Issue filed: https://bitbucket.org/galaxy/galaxy-central/issue/486 I expect many people to be caught out by this (back when I was debugging a proxy problem I was probably hitting this bug too). This is fixed in changeset 5188:52b59886df27, and will be available in our stable distribution the next time it's updated. --nate Regards, 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/
[galaxy-dev] Referencing data library directly from tool's input parameter dropdown.
Hello all. First of all thanks to Galaxy developers and supporters for this great tool -- I'm experimenting with adding my custom tools to galaxy and I'm very impressed with how simple galaxy makes this process. Some of the tools that I'm adding to my local instance take reference files as a parameter. These files are often large and fairly static. I understand that I can create a data library where users can select the reference file needed and import into history for analysis. However, I would like to know if it's possible for a tool's input parameter (dropdown) to enumerate these files from a public data-library (to avoid the steps needed to import from library into history) and have that file pathname become the value for my parameter? As an alternative, would it be possible to load such a drop down from files (of a certain type) existing at some predefined system path? Thanks in advance, -AR ___ 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/
