text manipulation Compute tool error
Hello On a local install of galaxy I am getting seemingly erroneous behavior from the text manipulation tool "Compute". It will compute the expression I set (c3-c2+1) but will concatenate it to the last column rather that create a new column. Also the job errors and is shown in red. I can get around the concatenation problem by using the Add Column tool but subsequent use of Compute also errors and its results are unavailable for further analysis though the output appears correct. Can you help? Mark This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.
I've received no replies to this post though clearly I must be doing something wrong since the tool would be useless if this were its normal behavior and judging from other posts people are using it. Please help. Thanks Mark From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of mark.rose@syngenta.com Sent: Sunday, January 06, 2013 4:32 PM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] text manipulation Compute tool error Hello On a local install of galaxy I am getting seemingly erroneous behavior from the text manipulation tool "Compute". It will compute the expression I set (c3-c2+1) but will concatenate it to the last column rather that create a new column. Also the job errors and is shown in red. I can get around the concatenation problem by using the Add Column tool but subsequent use of Compute also errors and its results are unavailable for further analysis though the output appears correct. Can you help? Mark ________________________________ This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.
Can you reproduce this behavior on our public server? If so, it'll be much easier for us to take a look at the issue. If you can't reproduce on our public server, then providing as many details as possible about the problem will provide the best chance for the list to help you. For instance: *what is the exact error that the tool is returning? *does it happen with all datasets or a particular dataset? *does it happen with all dataset types (e.g., interval, bed, gtf) or just some? Thanks, J. On Jan 14, 2013, at 11:46 AM, <mark.rose@syngenta.com> wrote:
I’ve received no replies to this post though clearly I must be doing something wrong since the tool would be useless if this were its normal behavior and judging from other posts people are using it. Please help.
Thanks
Mark
From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of mark.rose@syngenta.com Sent: Sunday, January 06, 2013 4:32 PM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] text manipulation Compute tool error
Hello
On a local install of galaxy I am getting seemingly erroneous behavior from the text manipulation tool “Compute”. It will compute the expression I set (c3-c2+1) but will concatenate it to the last column rather that create a new column. Also the job errors and is shown in red. I can get around the concatenation problem by using the Add Column tool but subsequent use of Compute also errors and its results are unavailable for further analysis though the output appears correct.
Can you help?
Mark
This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.
This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.___________________________________________________________ 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:
No. When I save the file I wish to manipulate from my local galaxy and upload it to the public galaxy and run "Compute" it works (i.e. a tab-delimited file is produced with the computed field occurring last, the job listing in the history is green, and the result is available for input into other tools). When I run it on my local galaxy a file is produced that has the computed field last ( which is accurately computed but it appears that the white space between it and the other columns appears to be possibly only a space and not a tab), no error is reported but the job listing in the history is red, and the output is not available for input into other tools. I've tried this on other tab-delimited files and it does the same thing. Mark From: Jeremy Goecks [mailto:jeremy.goecks@emory.edu] Sent: Monday, January 14, 2013 12:58 PM To: Rose Mark USRE Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] text manipulation Compute tool error Can you reproduce this behavior on our public server? If so, it'll be much easier for us to take a look at the issue. If you can't reproduce on our public server, then providing as many details as possible about the problem will provide the best chance for the list to help you. For instance: *what is the exact error that the tool is returning? *does it happen with all datasets or a particular dataset? *does it happen with all dataset types (e.g., interval, bed, gtf) or just some? Thanks, J. On Jan 14, 2013, at 11:46 AM, <mark.rose@syngenta.com<mailto:mark.rose@syngenta.com>> wrote: I've received no replies to this post though clearly I must be doing something wrong since the tool would be useless if this were its normal behavior and judging from other posts people are using it. Please help. Thanks Mark From: galaxy-dev-bounces@lists.bx.psu.edu<mailto:galaxy-dev-bounces@lists.bx.psu.edu> [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of mark.rose@syngenta.com<mailto:mark.rose@syngenta.com> Sent: Sunday, January 06, 2013 4:32 PM To: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: [galaxy-dev] text manipulation Compute tool error Hello On a local install of galaxy I am getting seemingly erroneous behavior from the text manipulation tool "Compute". It will compute the expression I set (c3-c2+1) but will concatenate it to the last column rather that create a new column. Also the job errors and is shown in red. I can get around the concatenation problem by using the Add Column tool but subsequent use of Compute also errors and its results are unavailable for further analysis though the output appears correct. Can you help? Mark ________________________________ This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. ________________________________ This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.___________________________________________________________ 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/ This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.
If you click on the bug icon for the failed dataset (click on the dataset name to open the dataset and find the icon), what is the error listed? If you click on the information icon, is there any additional output in the standard output or error? J. On Jan 14, 2013, at 2:50 PM, <mark.rose@syngenta.com> wrote:
No. When I save the file I wish to manipulate from my local galaxy and upload it to the public galaxy and run “Compute” it works (i.e. a tab-delimited file is produced with the computed field occurring last, the job listing in the history is green, and the result is available for input into other tools). When I run it on my local galaxy a file is produced that has the computed field last ( which is accurately computed but it appears that the white space between it and the other columns appears to be possibly only a space and not a tab), no error is reported but the job listing in the history is red, and the output is not available for input into other tools. I’ve tried this on other tab-delimited files and it does the same thing.
Mark
From: Jeremy Goecks [mailto:jeremy.goecks@emory.edu] Sent: Monday, January 14, 2013 12:58 PM To: Rose Mark USRE Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] text manipulation Compute tool error
Can you reproduce this behavior on our public server? If so, it'll be much easier for us to take a look at the issue.
If you can't reproduce on our public server, then providing as many details as possible about the problem will provide the best chance for the list to help you. For instance:
*what is the exact error that the tool is returning? *does it happen with all datasets or a particular dataset? *does it happen with all dataset types (e.g., interval, bed, gtf) or just some?
Thanks, J.
On Jan 14, 2013, at 11:46 AM, <mark.rose@syngenta.com> wrote:
I’ve received no replies to this post though clearly I must be doing something wrong since the tool would be useless if this were its normal behavior and judging from other posts people are using it. Please help.
Thanks
Mark
From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of mark.rose@syngenta.com Sent: Sunday, January 06, 2013 4:32 PM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] text manipulation Compute tool error
Hello
On a local install of galaxy I am getting seemingly erroneous behavior from the text manipulation tool “Compute”. It will compute the expression I set (c3-c2+1) but will concatenate it to the last column rather that create a new column. Also the job errors and is shown in red. I can get around the concatenation problem by using the Add Column tool but subsequent use of Compute also errors and its results are unavailable for further analysis though the output appears correct.
Can you help?
Mark
This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.
This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.___________________________________________________________ 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:
This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.
Ah, yes. I forgot about the bug icon. Sorry, still pretty new to galaxy. Here is the error message: /home/rosema1/Projects/galaxy-dist/lib/galaxy/__init__.py:79: UserWarning: Module markupsafe was already imported from /usr/lib/python2.7/dist-packages/markupsafe/__init__.pyc, but /home/rosema1/Projects/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg is being added to sys.path self.check_version_conflict() Stdout in the info link says: Creating column 4 with expression c3-c2+1 Kept 100.00% of 96 lines. Thanks Mark From: Jeremy Goecks [mailto:jeremy.goecks@emory.edu] Sent: Monday, January 14, 2013 2:56 PM To: Rose Mark USRE Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] text manipulation Compute tool error If you click on the bug icon for the failed dataset (click on the dataset name to open the dataset and find the icon), what is the error listed? If you click on the information icon, is there any additional output in the standard output or error? J. On Jan 14, 2013, at 2:50 PM, <mark.rose@syngenta.com<mailto:mark.rose@syngenta.com>> wrote: No. When I save the file I wish to manipulate from my local galaxy and upload it to the public galaxy and run "Compute" it works (i.e. a tab-delimited file is produced with the computed field occurring last, the job listing in the history is green, and the result is available for input into other tools). When I run it on my local galaxy a file is produced that has the computed field last ( which is accurately computed but it appears that the white space between it and the other columns appears to be possibly only a space and not a tab), no error is reported but the job listing in the history is red, and the output is not available for input into other tools. I've tried this on other tab-delimited files and it does the same thing. Mark From: Jeremy Goecks [mailto:jeremy.goecks@emory.edu] Sent: Monday, January 14, 2013 12:58 PM To: Rose Mark USRE Cc: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] text manipulation Compute tool error Can you reproduce this behavior on our public server? If so, it'll be much easier for us to take a look at the issue. If you can't reproduce on our public server, then providing as many details as possible about the problem will provide the best chance for the list to help you. For instance: *what is the exact error that the tool is returning? *does it happen with all datasets or a particular dataset? *does it happen with all dataset types (e.g., interval, bed, gtf) or just some? Thanks, J. On Jan 14, 2013, at 11:46 AM, <mark.rose@syngenta.com<mailto:mark.rose@syngenta.com>> wrote: I've received no replies to this post though clearly I must be doing something wrong since the tool would be useless if this were its normal behavior and judging from other posts people are using it. Please help. Thanks Mark From: galaxy-dev-bounces@lists.bx.psu.edu<mailto:galaxy-dev-bounces@lists.bx.psu.edu> [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of mark.rose@syngenta.com<mailto:mark.rose@syngenta.com> Sent: Sunday, January 06, 2013 4:32 PM To: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: [galaxy-dev] text manipulation Compute tool error Hello On a local install of galaxy I am getting seemingly erroneous behavior from the text manipulation tool "Compute". It will compute the expression I set (c3-c2+1) but will concatenate it to the last column rather that create a new column. Also the job errors and is shown in red. I can get around the concatenation problem by using the Add Column tool but subsequent use of Compute also errors and its results are unavailable for further analysis though the output appears correct. Can you help? Mark ________________________________ This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. ________________________________ This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.___________________________________________________________ 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/ ________________________________ This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.
The problem is that you have an egg conflict with an existing Python installation. The recommended way to fix this is to set up a virtual environment as discussed here: http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=show&redirect=Admin%2FConfig%2FPerformance%2FProduction+Server Best, J. On Jan 14, 2013, at 3:10 PM, <mark.rose@syngenta.com> wrote:
Ah, yes. I forgot about the bug icon. Sorry, still pretty new to galaxy.
Here is the error message:
/home/rosema1/Projects/galaxy-dist/lib/galaxy/__init__.py:79: UserWarning: Module markupsafe was already imported from /usr/lib/python2.7/dist-packages/markupsafe/__init__.pyc, but /home/rosema1/Projects/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg is being added to sys.path self.check_version_conflict()
Stdout in the info link says:
Creating column 4 with expression c3-c2+1 Kept 100.00% of 96 lines.
Thanks
Mark
From: Jeremy Goecks [mailto:jeremy.goecks@emory.edu] Sent: Monday, January 14, 2013 2:56 PM To: Rose Mark USRE Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] text manipulation Compute tool error
If you click on the bug icon for the failed dataset (click on the dataset name to open the dataset and find the icon), what is the error listed? If you click on the information icon, is there any additional output in the standard output or error?
J.
On Jan 14, 2013, at 2:50 PM, <mark.rose@syngenta.com> wrote:
No. When I save the file I wish to manipulate from my local galaxy and upload it to the public galaxy and run “Compute” it works (i.e. a tab-delimited file is produced with the computed field occurring last, the job listing in the history is green, and the result is available for input into other tools). When I run it on my local galaxy a file is produced that has the computed field last ( which is accurately computed but it appears that the white space between it and the other columns appears to be possibly only a space and not a tab), no error is reported but the job listing in the history is red, and the output is not available for input into other tools. I’ve tried this on other tab-delimited files and it does the same thing.
Mark
From: Jeremy Goecks [mailto:jeremy.goecks@emory.edu] Sent: Monday, January 14, 2013 12:58 PM To: Rose Mark USRE Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] text manipulation Compute tool error
Can you reproduce this behavior on our public server? If so, it'll be much easier for us to take a look at the issue.
If you can't reproduce on our public server, then providing as many details as possible about the problem will provide the best chance for the list to help you. For instance:
*what is the exact error that the tool is returning? *does it happen with all datasets or a particular dataset? *does it happen with all dataset types (e.g., interval, bed, gtf) or just some?
Thanks, J.
On Jan 14, 2013, at 11:46 AM, <mark.rose@syngenta.com> wrote:
I’ve received no replies to this post though clearly I must be doing something wrong since the tool would be useless if this were its normal behavior and judging from other posts people are using it. Please help.
Thanks
Mark
From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of mark.rose@syngenta.com Sent: Sunday, January 06, 2013 4:32 PM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] text manipulation Compute tool error
Hello
On a local install of galaxy I am getting seemingly erroneous behavior from the text manipulation tool “Compute”. It will compute the expression I set (c3-c2+1) but will concatenate it to the last column rather that create a new column. Also the job errors and is shown in red. I can get around the concatenation problem by using the Add Column tool but subsequent use of Compute also errors and its results are unavailable for further analysis though the output appears correct.
Can you help?
Mark
This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.
This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.___________________________________________________________ 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:
This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.
This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.
Yes, that did it. Thanks a lot! Mark From: Jeremy Goecks [mailto:jeremy.goecks@emory.edu] Sent: Monday, January 14, 2013 3:28 PM To: Rose Mark USRE Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] text manipulation Compute tool error The problem is that you have an egg conflict with an existing Python installation. The recommended way to fix this is to set up a virtual environment as discussed here: http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=show&redirect=Admin%2FConfig%2FPerformance%2FProduction+Server<http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=show&redirect=Admin/Config/Performance/Production+Server> Best, J. On Jan 14, 2013, at 3:10 PM, <mark.rose@syngenta.com<mailto:mark.rose@syngenta.com>> wrote: Ah, yes. I forgot about the bug icon. Sorry, still pretty new to galaxy. Here is the error message: /home/rosema1/Projects/galaxy-dist/lib/galaxy/__init__.py:79: UserWarning: Module markupsafe was already imported from /usr/lib/python2.7/dist-packages/markupsafe/__init__.pyc, but /home/rosema1/Projects/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg is being added to sys.path self.check_version_conflict() Stdout in the info link says: Creating column 4 with expression c3-c2+1 Kept 100.00% of 96 lines. Thanks Mark From: Jeremy Goecks [mailto:jeremy.goecks@emory.edu] Sent: Monday, January 14, 2013 2:56 PM To: Rose Mark USRE Cc: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] text manipulation Compute tool error If you click on the bug icon for the failed dataset (click on the dataset name to open the dataset and find the icon), what is the error listed? If you click on the information icon, is there any additional output in the standard output or error? J. On Jan 14, 2013, at 2:50 PM, <mark.rose@syngenta.com<mailto:mark.rose@syngenta.com>> wrote: No. When I save the file I wish to manipulate from my local galaxy and upload it to the public galaxy and run "Compute" it works (i.e. a tab-delimited file is produced with the computed field occurring last, the job listing in the history is green, and the result is available for input into other tools). When I run it on my local galaxy a file is produced that has the computed field last ( which is accurately computed but it appears that the white space between it and the other columns appears to be possibly only a space and not a tab), no error is reported but the job listing in the history is red, and the output is not available for input into other tools. I've tried this on other tab-delimited files and it does the same thing. Mark From: Jeremy Goecks [mailto:jeremy.goecks@emory.edu] Sent: Monday, January 14, 2013 12:58 PM To: Rose Mark USRE Cc: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] text manipulation Compute tool error Can you reproduce this behavior on our public server? If so, it'll be much easier for us to take a look at the issue. If you can't reproduce on our public server, then providing as many details as possible about the problem will provide the best chance for the list to help you. For instance: *what is the exact error that the tool is returning? *does it happen with all datasets or a particular dataset? *does it happen with all dataset types (e.g., interval, bed, gtf) or just some? Thanks, J. On Jan 14, 2013, at 11:46 AM, <mark.rose@syngenta.com<mailto:mark.rose@syngenta.com>> wrote: I've received no replies to this post though clearly I must be doing something wrong since the tool would be useless if this were its normal behavior and judging from other posts people are using it. Please help. Thanks Mark From: galaxy-dev-bounces@lists.bx.psu.edu<mailto:galaxy-dev-bounces@lists.bx.psu.edu> [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of mark.rose@syngenta.com<mailto:mark.rose@syngenta.com> Sent: Sunday, January 06, 2013 4:32 PM To: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: [galaxy-dev] text manipulation Compute tool error Hello On a local install of galaxy I am getting seemingly erroneous behavior from the text manipulation tool "Compute". It will compute the expression I set (c3-c2+1) but will concatenate it to the last column rather that create a new column. Also the job errors and is shown in red. I can get around the concatenation problem by using the Add Column tool but subsequent use of Compute also errors and its results are unavailable for further analysis though the output appears correct. Can you help? Mark ________________________________ This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. ________________________________ This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.___________________________________________________________ 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/ ________________________________ This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. ________________________________ This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.
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Jeremy Goecks -
mark.rose＠syngenta.com