Re: [galaxy-dev] copy/import shared history
Hi Martin, Thanks for pointing out I actually downloaded the dev branch instead of the stable version. Best Le-Shin > On Feb 17, 2016, at 10:05 AM, Martin Čech wrote: > > Le-Shin, > > 'git clone https://github.com/galaxyproject/galaxy > <https://github.com/galaxyproject/galaxy>' command will get you on the 'dev' > branch of Galaxy. Unless you want to develop new features I recommend you to > use the latest Galaxy release, described here: > https://docs.galaxyproject.org/en/master/releases/15.10_announce.html > <https://docs.galaxyproject.org/en/master/releases/15.10_announce.html> > > We are also tracking the bug you described on this ticket: > https://github.com/galaxyproject/galaxy/issues/1743 > <https://github.com/galaxyproject/galaxy/issues/1743> > > Best > > Martin > > > > On Tue, Feb 16, 2016 at 10:22 PM Le-Shin Wu <mailto:les...@gmail.com>> wrote: > Hi Martin, > > I used "git clone” to get the galaxy from github site, so I think our galaxy > version should be the latest. I didn’t see any error from the JS console but > I found if I didn’t use apache as the proxy, the "copy shared history” > function seems working. I am not sure what went wrong for the apache proxy > because I don’t have any other issue except this “copy shared history” > function. Thanks for your information. > > Best > > Le-Shin > > >> On Feb 16, 2016, at 1:02 PM, Martin Čech > <mailto:mar...@bx.psu.edu>> wrote: >> > >> Hi LW, >> >> 1) The described 'copy' feature works well for me on usegalaxy.org >> <http://usegalaxy.org/>. However the 'view and import' activity does fail >> for me too. We will look into that. What version of Galaxy are you using? Do >> you see any errors in the JS console of your browser? >> 2) 'purge' does only remove all roles from the group, not the group itself. >> Galaxy does not delete entities, only marks them as deleted in the DB. >> 3) should be fixed after merge of >> https://github.com/galaxyproject/tools-iuc/pull/596 >> <https://github.com/galaxyproject/tools-iuc/pull/596> >> >> Thank you for using Galaxy >> >> Martin >> > >> On Tue, Feb 16, 2016 at 12:45 PM Le-Shin Wu > <mailto:les...@gmail.com>> wrote: > >> Hi, >> >> I’ve recently installed a new galaxy server and I found some weird behaviors >> of admin jobs. >> >> First, a shared history can not be copied as a new history. For example, >> user A shared one of his history with user B. User B can see this shared >> history through “histories shred with me” link, but when user B clicks >> “copy” of this history nothing happened. However, user B can view this >> history if he clicks “view” but if he then clicks “import history”, a new >> galaxy home page will be displayed on the center panel (as shown in the >> attached screenshot). >> >> Second, the administer can only delete groups but he can not purge those >> deleted groups. In other words, when the administer clicks the “purge” >> button of a deleted group, nothing will happen on this group. It still shows >> on the table with status as “deleted” >> >> Third, when installed the “package_fontconfig_2_11_1” through tool shed, the >> status of this package always shows as “installing tool dependencies”. We >> restarted our galaxy server several times but this message never went away >> (it always shows on the “monitor installing repositories” page). >> >> We really have no idea how to fix these strange behaviors and the web log >> file also don’t have any error message. Any suggestion? Thank you. >> >> Best >> >> LW >> > >> > >> ___ >> 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/ <https://lists.galaxyproject.org/> >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> <http://galaxyproject.org/search/mailinglists/> ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] copy/import shared history
Hi Martin, I used "git clone” to get the galaxy from github site, so I think our galaxy version should be the latest. I didn’t see any error from the JS console but I found if I didn’t use apache as the proxy, the "copy shared history” function seems working. I am not sure what went wrong for the apache proxy because I don’t have any other issue except this “copy shared history” function. Thanks for your information. Best Le-Shin > On Feb 16, 2016, at 1:02 PM, Martin Čech wrote: > > Hi LW, > > 1) The described 'copy' feature works well for me on usegalaxy.org > <http://usegalaxy.org/>. However the 'view and import' activity does fail for > me too. We will look into that. What version of Galaxy are you using? Do you > see any errors in the JS console of your browser? > 2) 'purge' does only remove all roles from the group, not the group itself. > Galaxy does not delete entities, only marks them as deleted in the DB. > 3) should be fixed after merge of > https://github.com/galaxyproject/tools-iuc/pull/596 > <https://github.com/galaxyproject/tools-iuc/pull/596> > > Thank you for using Galaxy > > Martin > > On Tue, Feb 16, 2016 at 12:45 PM Le-Shin Wu <mailto:les...@gmail.com>> wrote: > Hi, > > I’ve recently installed a new galaxy server and I found some weird behaviors > of admin jobs. > > First, a shared history can not be copied as a new history. For example, user > A shared one of his history with user B. User B can see this shared history > through “histories shred with me” link, but when user B clicks “copy” of this > history nothing happened. However, user B can view this history if he clicks > “view” but if he then clicks “import history”, a new galaxy home page will be > displayed on the center panel (as shown in the attached screenshot). > > Second, the administer can only delete groups but he can not purge those > deleted groups. In other words, when the administer clicks the “purge” button > of a deleted group, nothing will happen on this group. It still shows on the > table with status as “deleted” > > Third, when installed the “package_fontconfig_2_11_1” through tool shed, the > status of this package always shows as “installing tool dependencies”. We > restarted our galaxy server several times but this message never went away > (it always shows on the “monitor installing repositories” page). > > We really have no idea how to fix these strange behaviors and the web log > file also don’t have any error message. Any suggestion? Thank you. > > Best > > LW > > > ___ > 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/ <https://lists.galaxyproject.org/> > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > <http://galaxyproject.org/search/mailinglists/> ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] dramm.py error
Hi Nate, The tool ID is simply as "upload1" (I just tried to upload a file) and user email address is simply as "les...@gmail.com". The original job name before applying the lambda function is something like "g6_upload1_les...@gmail.com". I am not sure why this job_name will create the problem. But after I removing the job_wrapper.user out of the job_name in __init__.py and dramm.py, I can run jobs on our UGE with problems. The only issue for this approach is that there is no actual user information inside the UGE job name anymore. Thanks LW On Fri, Feb 5, 2016 at 1:23 PM, Nate Coraor wrote: > On Thu, Feb 4, 2016 at 1:21 PM, Le-shin Wu wrote: > >> Hi, >> >> I was trying to setup a galaxy server and connect to our UGE cluster. If >> I setup the default job runner as "local", our galaxy server works >> properly. But if I change the default job runner as "drmaa", our galaxy >> server throws out the following error message. It looks like drmaa.py has >> unicode decoding issue. I wonder does someone have the same problem before >> and how can I fix it. The python version we are using is 2.7.10. Thank >> you. >> >> galaxy.jobs.runners ERROR 2016-02-04 10:49:44,689 (3) Unhandled exception >> calling queue_job >> Traceback (most recent call last): >> File "/home/c226089/galaxy/lib/galaxy/jobs/runners/__init__.py", line >> 103, in run_next >> method(arg) >> File "/home/c226089/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 135, >> in queue_job >> job_name = ''.join( map( lambda x: x if x in ( string.letters + >> string.digits + '_' ) else '_', job_name ) ) >> File "/home/c226089/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 135, >> in >> job_name = ''.join( map( lambda x: x if x in ( string.letters + >> string.digits + '_' ) else '_', job_name ) ) >> UnicodeDecodeError: 'ascii' codec can't decode byte 0xaa in position 52: >> ordinal not in range(128) >> > > Hi, > > Does your tool ID or user email address contain a unicode character? > > Regardless, this is a bug and we can fix it, I just want to verify the > problem. > > Thanks, > --nate > > >> >> >> Best >> >> LW >> >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] dramm.py error
Hi, I was trying to setup a galaxy server and connect to our UGE cluster. If I setup the default job runner as "local", our galaxy server works properly. But if I change the default job runner as "drmaa", our galaxy server throws out the following error message. It looks like drmaa.py has unicode decoding issue. I wonder does someone have the same problem before and how can I fix it. The python version we are using is 2.7.10. Thank you. galaxy.jobs.runners ERROR 2016-02-04 10:49:44,689 (3) Unhandled exception calling queue_job Traceback (most recent call last): File "/home/c226089/galaxy/lib/galaxy/jobs/runners/__init__.py", line 103, in run_next method(arg) File "/home/c226089/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 135, in queue_job job_name = ''.join( map( lambda x: x if x in ( string.letters + string.digits + '_' ) else '_', job_name ) ) File "/home/c226089/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 135, in job_name = ''.join( map( lambda x: x if x in ( string.letters + string.digits + '_' ) else '_', job_name ) ) UnicodeDecodeError: 'ascii' codec can't decode byte 0xaa in position 52: ordinal not in range(128) Best LW ___ 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/
