Impossible to add a (new) tool in a workflow (in edition mode)
Hello, For one of my tools that I have added to my local instance of Galaxy, I can not add this tool in the editing workflow. When I click on the tool name in the "tools" windows on the left, it does not appear in the editing workflow. Do you have any idea? Thank you in advance, Sarah Maman
Do you see any errors in Galaxy's paster.log, or in the javascript console? -Dannon On Dec 11, 2012, at 8:40 AM, Sarah Maman <sarah.maman@toulouse.inra.fr> wrote:
Hello,
For one of my tools that I have added to my local instance of Galaxy, I can not add this tool in the editing workflow. When I click on the tool name in the "tools" windows on the left, it does not appear in the editing workflow.
Do you have any idea?
Thank you in advance, Sarah Maman ___________________________________________________________ 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:
Thanks Danon, But I have no error generated in my error log file (logs of run.sh): [11/Dec/2012:16:39:09 +0200] "GET /galaxy/workflow HTTP/1.1" 200 - "http://URL/galaxy/root" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0" IP - - [11/Dec/2012:16:39:11 +0200] "GET /galaxy/workflow/editor?id=7085c9c37b8829fc HTTP/1.1" 200 - "http://URL/galaxy/workflow" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0" IP - - [11/Dec/2012:16:39:12 +0200] "GET /galaxy/workflow/get_datatypes?_=1355240375711 HTTP/1.1" 200 - "http://URL/galaxy/workflow/editor?id=7085c9c37b8829fc" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0" IP - - [11/Dec/2012:16:39:12 +0200] "GET /galaxy/workflow/load_workflow?id=7085c9c37b8829fc&_=1355240375756 HTTP/1.1" 200 - "http://URL/galaxy/workflow/editor?id=7085c9c37b8829fc" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0" IP - - [11/Dec/2012:16:39:17 +0200] "GET /galaxy/workflow/get_new_module_info?type=tool&tool_id=BWA_miRNA&_=true HTTP/1.1" 200 - "http://URL/galaxy/workflow/editor?id=7085c9c37b8829fc" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0" Others actions are listed by not my click on this tool's name. Is paster.log file a default file of Galaxy? Where could I find this file ? Sarah Dannon Baker a écrit :
Do you see any errors in Galaxy's paster.log, or in the javascript console?
-Dannon
On Dec 11, 2012, at 8:40 AM, Sarah Maman <sarah.maman@toulouse.inra.fr> wrote:
Hello,
For one of my tools that I have added to my local instance of Galaxy, I can not add this tool in the editing workflow. When I click on the tool name in the "tools" windows on the left, it does not appear in the editing workflow.
Do you have any idea?
Thank you in advance, Sarah Maman ___________________________________________________________ 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:
The paster.log is just the file for the output you've copied below when running daemonized -- if you're running in the foreground it just gets sent there instead of to the file. So, no obvious errors there. Could you check for javascript console errors? And, if you'd like, feel free to send the tool xml to me directly and I'll try to see if I can reproduce the issue. -Dannon On Dec 11, 2012, at 10:47 AM, Sarah Maman <sarah.maman@toulouse.inra.fr> wrote:
Thanks Danon,
But I have no error generated in my error log file (logs of run.sh):
[11/Dec/2012:16:39:09 +0200] "GET /galaxy/workflow HTTP/1.1" 200 - "http://URL/galaxy/root" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0" IP - - [11/Dec/2012:16:39:11 +0200] "GET /galaxy/workflow/editor?id=7085c9c37b8829fc HTTP/1.1" 200 - "http://URL/galaxy/workflow" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0" IP - - [11/Dec/2012:16:39:12 +0200] "GET /galaxy/workflow/get_datatypes?_=1355240375711 HTTP/1.1" 200 - "http://URL/galaxy/workflow/editor?id=7085c9c37b8829fc" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0" IP - - [11/Dec/2012:16:39:12 +0200] "GET /galaxy/workflow/load_workflow?id=7085c9c37b8829fc&_=1355240375756 HTTP/1.1" 200 - "http://URL/galaxy/workflow/editor?id=7085c9c37b8829fc" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0" IP - - [11/Dec/2012:16:39:17 +0200] "GET /galaxy/workflow/get_new_module_info?type=tool&tool_id=BWA_miRNA&_=true HTTP/1.1" 200 - "http://URL/galaxy/workflow/editor?id=7085c9c37b8829fc" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0"
Others actions are listed by not my click on this tool's name. Is paster.log file a default file of Galaxy? Where could I find this file ?
Sarah
Dannon Baker a écrit :
Do you see any errors in Galaxy's paster.log, or in the javascript console?
-Dannon
On Dec 11, 2012, at 8:40 AM, Sarah Maman <sarah.maman@toulouse.inra.fr> wrote:
Hello,
For one of my tools that I have added to my local instance of Galaxy, I can not add this tool in the editing workflow. When I click on the tool name in the "tools" windows on the left, it does not appear in the editing workflow.
Do you have any idea?
Thank you in advance, Sarah Maman ___________________________________________________________ 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:
Dannon, Here is myjavascript console errors : SyntaxError: missing ) after argument list : /* ool( 'sm_miRNA_join_annot', '* Construction de la matrice d'annotations' ) */ /*editor...8829fc# (ligne 1, col. 60)*/ I replaced this syntax "Construction de la matrice d'annotations" by the latter "Construction de la matrice d annotations", and thank you, now it works! Thanks a lot, Sarah Dannon Baker a écrit :
The paster.log is just the file for the output you've copied below when running daemonized -- if you're running in the foreground it just gets sent there instead of to the file. So, no obvious errors there. Could you check for javascript console errors?
And, if you'd like, feel free to send the tool xml to me directly and I'll try to see if I can reproduce the issue.
-Dannon
On Dec 11, 2012, at 10:47 AM, Sarah Maman <sarah.maman@toulouse.inra.fr> wrote:
Thanks Danon,
But I have no error generated in my error log file (logs of run.sh):
[11/Dec/2012:16:39:09 +0200] "GET /galaxy/workflow HTTP/1.1" 200 - "http://URL/galaxy/root" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0" IP - - [11/Dec/2012:16:39:11 +0200] "GET /galaxy/workflow/editor?id=7085c9c37b8829fc HTTP/1.1" 200 - "http://URL/galaxy/workflow" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0" IP - - [11/Dec/2012:16:39:12 +0200] "GET /galaxy/workflow/get_datatypes?_=1355240375711 HTTP/1.1" 200 - "http://URL/galaxy/workflow/editor?id=7085c9c37b8829fc" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0" IP - - [11/Dec/2012:16:39:12 +0200] "GET /galaxy/workflow/load_workflow?id=7085c9c37b8829fc&_=1355240375756 HTTP/1.1" 200 - "http://URL/galaxy/workflow/editor?id=7085c9c37b8829fc" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0" IP - - [11/Dec/2012:16:39:17 +0200] "GET /galaxy/workflow/get_new_module_info?type=tool&tool_id=BWA_miRNA&_=true HTTP/1.1" 200 - "http://URL/galaxy/workflow/editor?id=7085c9c37b8829fc" "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0"
Others actions are listed by not my click on this tool's name. Is paster.log file a default file of Galaxy? Where could I find this file ?
Sarah
Dannon Baker a écrit :
Do you see any errors in Galaxy's paster.log, or in the javascript console?
-Dannon
On Dec 11, 2012, at 8:40 AM, Sarah Maman <sarah.maman@toulouse.inra.fr> wrote:
Hello,
For one of my tools that I have added to my local instance of Galaxy, I can not add this tool in the editing workflow. When I click on the tool name in the "tools" windows on the left, it does not appear in the editing workflow.
Do you have any idea?
Thank you in advance, Sarah Maman ___________________________________________________________ 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:
participants (2)
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Dannon Baker -
Sarah Maman