Hi all, Recently i installed RSEM into Galaxy. The problem is that now i cannot find the tool when i open "my" galaxy in my computer. I checked and rsem folder is inside the tool folder. Any suggestions? Thanks, Alicia. -- Alicia R. Pérez-Porro PhD student Giribet lab Department of Organismic and Evolutionary Biology MCZ labs Harvard University 26 Oxford St, Cambridge MA 02138 phone: +1 617-496-5308 fax: +1 617-495-5667 www.oeb.harvard.edu/faculty/giribet/ Department of Marine Ecology Center for Advanced Studies of Blanes (CEAB-CSIC) C/Accés Cala St. Francesc 14 17300 Blanes, Girona, SPAIN phone: +34 972 336 101 fax: +34 972 337 806 www.ceab.csic.es
Alicia, Some relevant details usually make it easier for list members to help you - please see http://wiki.g2.bx.psu.edu/Support#Public_mailing_list_Q_.26_A_discussions Did you load the offending tool from a toolshed or is it a tool wrapper you wrote yourself? If the latter, I have two suggestions: 1) Search paster.log for your tool name and make sure it got correctly loaded when you restarted Galaxy - xml syntax errors like misplaced < characters will break the tool loading process. 2) if the log shows that it loaded, make sure you refresh the tool frame in your browser after restarting Galaxy - eg clicking the "analyse data" tab will get rid of the old cached copy. On Sat, Oct 6, 2012 at 10:02 AM, Alicia R. Pérez-Porro <alicia.r.perezporro@gmail.com> wrote:
Hi all,
Recently i installed RSEM into Galaxy. The problem is that now i cannot find the tool when i open "my" galaxy in my computer. I checked and rsem folder is inside the tool folder. Any suggestions?
Thanks, Alicia.
-- Alicia R. Pérez-Porro PhD student
Giribet lab Department of Organismic and Evolutionary Biology MCZ labs Harvard University 26 Oxford St, Cambridge MA 02138 phone: +1 617-496-5308 fax: +1 617-495-5667 www.oeb.harvard.edu/faculty/giribet/
Department of Marine Ecology Center for Advanced Studies of Blanes (CEAB-CSIC) C/Accés Cala St. Francesc 14 17300 Blanes, Girona, SPAIN phone: +34 972 336 101 fax: +34 972 337 806 www.ceab.csic.es
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
Hi Alicia, At the moment you have to install the wrapper manually. That is, the current version of the RSEM won't automatically install the rsem binaries for you. We are working on updating the tool from the tool shed. The readme file within the tarball provides instructions on what version of RSEM to install and other details. We ll keep you posted as soon as we update the tool so things will be done for you much like the other newer tools in the tool shed. Thank you for using RSEM and please let me know how it goes. Victor On Oct 5, 2012, at 7:14 PM, Ross <ross.lazarus@gmail.com> wrote:
Alicia,
Some relevant details usually make it easier for list members to help you - please see http://wiki.g2.bx.psu.edu/Support#Public_mailing_list_Q_.26_A_discussions
Did you load the offending tool from a toolshed or is it a tool wrapper you wrote yourself? If the latter, I have two suggestions:
1) Search paster.log for your tool name and make sure it got correctly loaded when you restarted Galaxy - xml syntax errors like misplaced < characters will break the tool loading process.
2) if the log shows that it loaded, make sure you refresh the tool frame in your browser after restarting Galaxy - eg clicking the "analyse data" tab will get rid of the old cached copy.
On Sat, Oct 6, 2012 at 10:02 AM, Alicia R. Pérez-Porro <alicia.r.perezporro@gmail.com> wrote:
Hi all,
Recently i installed RSEM into Galaxy. The problem is that now i cannot find the tool when i open "my" galaxy in my computer. I checked and rsem folder is inside the tool folder. Any suggestions?
Thanks, Alicia.
-- Alicia R. Pérez-Porro PhD student
Giribet lab Department of Organismic and Evolutionary Biology MCZ labs Harvard University 26 Oxford St, Cambridge MA 02138 phone: +1 617-496-5308 fax: +1 617-495-5667 www.oeb.harvard.edu/faculty/giribet/
Department of Marine Ecology Center for Advanced Studies of Blanes (CEAB-CSIC) C/Accés Cala St. Francesc 14 17300 Blanes, Girona, SPAIN phone: +34 972 336 101 fax: +34 972 337 806 www.ceab.csic.es
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi there Alicia! To find the tool in the Galaxy tool search, first you have to put your tool files in tools with .xml files then you have to edit tool_conf.xml file. Here's the step by step tutorial: http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial Regards, Sachit On Fri, Oct 5, 2012 at 8:55 PM, Victor <ruotti@wisc.edu> wrote:
Hi Alicia, At the moment you have to install the wrapper manually. That is, the current version of the RSEM won't automatically install the rsem binaries for you. We are working on updating the tool from the tool shed. The readme file within the tarball provides instructions on what version of RSEM to install and other details. We ll keep you posted as soon as we update the tool so things will be done for you much like the other newer tools in the tool shed. Thank you for using RSEM and please let me know how it goes.
Victor
On Oct 5, 2012, at 7:14 PM, Ross <ross.lazarus@gmail.com> wrote:
Alicia,
Some relevant details usually make it easier for list members to help you - please see
http://wiki.g2.bx.psu.edu/Support#Public_mailing_list_Q_.26_A_discussions
Did you load the offending tool from a toolshed or is it a tool wrapper you wrote yourself? If the latter, I have two suggestions:
1) Search paster.log for your tool name and make sure it got correctly loaded when you restarted Galaxy - xml syntax errors like misplaced < characters will break the tool loading process.
2) if the log shows that it loaded, make sure you refresh the tool frame in your browser after restarting Galaxy - eg clicking the "analyse data" tab will get rid of the old cached copy.
On Sat, Oct 6, 2012 at 10:02 AM, Alicia R. Pérez-Porro <alicia.r.perezporro@gmail.com> wrote:
Hi all,
Recently i installed RSEM into Galaxy. The problem is that now i cannot find the tool when i open "my" galaxy
in my
computer. I checked and rsem folder is inside the tool folder. Any suggestions?
Thanks, Alicia.
-- Alicia R. Pérez-Porro PhD student
Giribet lab Department of Organismic and Evolutionary Biology MCZ labs Harvard University 26 Oxford St, Cambridge MA 02138 phone: +1 617-496-5308 fax: +1 617-495-5667 www.oeb.harvard.edu/faculty/giribet/
Department of Marine Ecology Center for Advanced Studies of Blanes (CEAB-CSIC) C/Accés Cala St. Francesc 14 17300 Blanes, Girona, SPAIN phone: +34 972 336 101 fax: +34 972 337 806 www.ceab.csic.es
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (4)
-
Alicia R. Pérez-Porro -
Ross -
Sachit Adhikari -
Victor