copy/import shared history
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
Hi LW, 1) The described 'copy' feature works well for me on 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 Thank you for using Galaxy Martin On Tue, Feb 16, 2016 at 12:45 PM Le-Shin Wu <leshin@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
[image: Screen Shot 2016-02-15 at 10.35.25 PM.png] ___________________________________________________________ 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/
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I created an issue for the history import problems, you can track it (and contribute) here https://github.com/galaxyproject/galaxy/issues/1743 thanks M. On Tue, Feb 16, 2016 at 1:02 PM Martin Čech <marten@bx.psu.edu> wrote:
Hi LW,
1) The described 'copy' feature works well for me on 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
Thank you for using Galaxy
Martin
On Tue, Feb 16, 2016 at 12:45 PM Le-Shin Wu <leshin@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
[image: Screen Shot 2016-02-15 at 10.35.25 PM.png]
___________________________________________________________
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/
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 <marten@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 <leshin@gmail.com <mailto:leshin@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
<Screen Shot 2016-02-15 at 10.35.25 PM.png> ___________________________________________________________ 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/>
Le-Shin, 'git clone 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 We are also tracking the bug you described on this ticket: https://github.com/galaxyproject/galaxy/issues/1743 Best Martin On Tue, Feb 16, 2016 at 10:22 PM Le-Shin Wu <leshin@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 <marten@bx.psu.edu> wrote:
Hi LW,
1) The described 'copy' feature works well for me on 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
Thank you for using Galaxy
Martin
On Tue, Feb 16, 2016 at 12:45 PM Le-Shin Wu <leshin@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
<Screen Shot 2016-02-15 at 10.35.25 PM.png>
___________________________________________________________
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/
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 <marten@bx.psu.edu> 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 <leshin@gmail.com <mailto:leshin@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 <marten@bx.psu.edu <mailto:marten@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 <leshin@gmail.com <mailto:leshin@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
<Screen Shot 2016-02-15 at 10.35.25 PM.png>
___________________________________________________________ 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/>
participants (2)
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Le-Shin Wu -
Martin Čech