Is there a way to install a tool from toolshed in cloudman without using commands?
Hello, I launched a new Cloudman instance last week to analyse my RNA-seq data. I uploaded and cleaned my data, but could not run Tophat and Cufflinks due to the "Broken symbolic links" problem (https://bitbucket.org/galaxy/cloudman/issue/6/tool-default-symbolic-links-to...). I have completed running Tophat2 on the public server. Now, I like to install edgeR (http://toolshed.g2.bx.psu.edu/repository?repository_id=0c447003da85ae19) from the toolshed for further analyses. I cannot find a way to install that tool in my cloudman instance. My background is in psychiatry and I do not have any knowledge of Linux commands. Is there a way to install a tool (edgeR) from the toolshed without using command lines? Any help is greatly appreciated. Thank you. Best wishes, Anto Anto Rajkumar, MD, DNB, MRCPsych, PhD fellow, Department of Biomedicine, Aarhus university, 8000 C, Aarhus, Denmark. Ph (office) : 045- 87167292 E-mail: APR@hum-gen.au.dk
Hi Anto, Yes, you should be able to create an admin user for your galaxy installation via the cloudman admin panel (http://<your_ec2_instance>/cloud/admin) in as an admin. Once you're an admin user, you'll see the toolshed installation stuff in the galaxy admin panel. -Dannon On Fri, Aug 16, 2013 at 6:03 AM, Anto Praveen Rajkumar Rajamani < APR@hum-gen.au.dk> wrote:
Hello,
I launched a new Cloudman instance last week to analyse my RNA-seq data. I uploaded and cleaned my data, but could not run Tophat and Cufflinks due to the "Broken symbolic links" problem ( https://bitbucket.org/galaxy/cloudman/issue/6/tool-default-symbolic-links-to... ). I have completed running Tophat2 on the public server. Now, I like to install edgeR ( http://toolshed.g2.bx.psu.edu/repository?repository_id=0c447003da85ae19) from the toolshed for further analyses. I cannot find a way to install that tool in my cloudman instance. My background is in psychiatry and I do not have any knowledge of Linux commands. Is there a way to install a tool (edgeR) from the toolshed without using command lines? Any help is greatly appreciated. Thank you.
Best wishes, Anto
Anto Rajkumar, MD, DNB, MRCPsych, PhD fellow, Department of Biomedicine, Aarhus university, 8000 C, Aarhus, Denmark. Ph (office) : 045- 87167292 E-mail: APR@hum-gen.au.dk
___________________________________________________________ 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/
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Hi Dannon, I visited admin panel of http://<my_ec2_instance>/cloud/admin Under Add Galaxy admin users, I typed my email and pushed the "Add admin users" tab. I get the following message, Either no acceptable admin values provided ([]) or Galaxy service not found Current Galaxy admin remains as cloud@galaxyproject.org. Where do I go wrong? How do I create the new admin user? Best wishes, Anto ________________________________ From: Dannon Baker [dannon.baker@gmail.com] Sent: 16 August 2013 14:04 To: Anto Praveen Rajkumar Rajamani Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Is there a way to install a tool from toolshed in cloudman without using commands? Hi Anto, Yes, you should be able to create an admin user for your galaxy installation via the cloudman admin panel (http://<your_ec2_instance>/cloud/admin) in as an admin. Once you're an admin user, you'll see the toolshed installation stuff in the galaxy admin panel. -Dannon On Fri, Aug 16, 2013 at 6:03 AM, Anto Praveen Rajkumar Rajamani <APR@hum-gen.au.dk<mailto:APR@hum-gen.au.dk>> wrote: Hello, I launched a new Cloudman instance last week to analyse my RNA-seq data. I uploaded and cleaned my data, but could not run Tophat and Cufflinks due to the "Broken symbolic links" problem (https://bitbucket.org/galaxy/cloudman/issue/6/tool-default-symbolic-links-to...). I have completed running Tophat2 on the public server. Now, I like to install edgeR (http://toolshed.g2.bx.psu.edu/repository?repository_id=0c447003da85ae19) from the toolshed for further analyses. I cannot find a way to install that tool in my cloudman instance. My background is in psychiatry and I do not have any knowledge of Linux commands. Is there a way to install a tool (edgeR) from the toolshed without using command lines? Any help is greatly appreciated. Thank you. Best wishes, Anto Anto Rajkumar, MD, DNB, MRCPsych, PhD fellow, Department of Biomedicine, Aarhus university, 8000 C, Aarhus, Denmark. Ph (office) : 045- 87167292 E-mail: APR@hum-gen.au.dk<mailto:APR@hum-gen.au.dk> ___________________________________________________________ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
The only way I'm able to reproduce this on my end is by clicking "Add admin users" with the box next to it completely empty: [image: Inline image 1] You're seeing this error, and you have 'yourname@domain.com' in the box? On Fri, Aug 16, 2013 at 9:14 AM, Anto Praveen Rajkumar Rajamani < APR@hum-gen.au.dk> wrote:
Hi Dannon,
I visited admin panel of http://<my_ec2_instance>/cloud/admin Under Add Galaxy admin users, I typed my email and pushed the "Add admin users" tab. I get the following message, Either no acceptable admin values provided ([]) or Galaxy service not found Current Galaxy admin remains as cloud@galaxyproject.org. Where do I go wrong? How do I create the new admin user?
Best wishes, Anto
------------------------------ *From:* Dannon Baker [dannon.baker@gmail.com] *Sent:* 16 August 2013 14:04 *To:* Anto Praveen Rajkumar Rajamani *Cc:* galaxy-dev@bx.psu.edu *Subject:* Re: [galaxy-dev] Is there a way to install a tool from toolshed in cloudman without using commands?
Hi Anto,
Yes, you should be able to create an admin user for your galaxy installation via the cloudman admin panel (http://<your_ec2_instance>/cloud/admin) in as an admin. Once you're an admin user, you'll see the toolshed installation stuff in the galaxy admin panel.
-Dannon
On Fri, Aug 16, 2013 at 6:03 AM, Anto Praveen Rajkumar Rajamani < APR@hum-gen.au.dk> wrote:
Hello,
I launched a new Cloudman instance last week to analyse my RNA-seq data. I uploaded and cleaned my data, but could not run Tophat and Cufflinks due to the "Broken symbolic links" problem ( https://bitbucket.org/galaxy/cloudman/issue/6/tool-default-symbolic-links-to... ). I have completed running Tophat2 on the public server. Now, I like to install edgeR ( http://toolshed.g2.bx.psu.edu/repository?repository_id=0c447003da85ae19) from the toolshed for further analyses. I cannot find a way to install that tool in my cloudman instance. My background is in psychiatry and I do not have any knowledge of Linux commands. Is there a way to install a tool (edgeR) from the toolshed without using command lines? Any help is greatly appreciated. Thank you.
Best wishes, Anto
Anto Rajkumar, MD, DNB, MRCPsych, PhD fellow, Department of Biomedicine, Aarhus university, 8000 C, Aarhus, Denmark. Ph (office) : 045- 87167292 E-mail: APR@hum-gen.au.dk
___________________________________________________________ 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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Dannon, Thank you for the kind reply. I see this error, while I have "registeredemailaddress@ec2domain.com" in the box. My registered email address is APR@hum-gen.au.dk. I use the domain name from my aws ec2 instance. Where do I go wrong? Best wishes, Anto Anto Rajkumar, MD, DNB, MRCPsych, PhD fellow, Department of Biomedicine, Aarhus university, 8000 C, Aarhus, Denmark. E-mail: APR@hum-gen.au.dk ________________________________ From: Dannon Baker [dannon.baker@gmail.com] Sent: 16 August 2013 15:53 To: Anto Praveen Rajkumar Rajamani Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Is there a way to install a tool from toolshed in cloudman without using commands? The only way I'm able to reproduce this on my end is by clicking "Add admin users" with the box next to it completely empty: [Inline image 1] You're seeing this error, and you have 'yourname@domain.com<mailto:yourname@domain.com>' in the box? On Fri, Aug 16, 2013 at 9:14 AM, Anto Praveen Rajkumar Rajamani <APR@hum-gen.au.dk<mailto:APR@hum-gen.au.dk>> wrote: Hi Dannon, I visited admin panel of http://<my_ec2_instance>/cloud/admin Under Add Galaxy admin users, I typed my email and pushed the "Add admin users" tab. I get the following message, Either no acceptable admin values provided ([]) or Galaxy service not found Current Galaxy admin remains as cloud@galaxyproject.org<mailto:cloud@galaxyproject.org>. Where do I go wrong? How do I create the new admin user? Best wishes, Anto ________________________________ From: Dannon Baker [dannon.baker@gmail.com<mailto:dannon.baker@gmail.com>] Sent: 16 August 2013 14:04 To: Anto Praveen Rajkumar Rajamani Cc: galaxy-dev@bx.psu.edu<mailto:galaxy-dev@bx.psu.edu> Subject: Re: [galaxy-dev] Is there a way to install a tool from toolshed in cloudman without using commands? Hi Anto, Yes, you should be able to create an admin user for your galaxy installation via the cloudman admin panel (http://<your_ec2_instance>/cloud/admin) in as an admin. Once you're an admin user, you'll see the toolshed installation stuff in the galaxy admin panel. -Dannon On Fri, Aug 16, 2013 at 6:03 AM, Anto Praveen Rajkumar Rajamani <APR@hum-gen.au.dk<mailto:APR@hum-gen.au.dk>> wrote: Hello, I launched a new Cloudman instance last week to analyse my RNA-seq data. I uploaded and cleaned my data, but could not run Tophat and Cufflinks due to the "Broken symbolic links" problem (https://bitbucket.org/galaxy/cloudman/issue/6/tool-default-symbolic-links-to...). I have completed running Tophat2 on the public server. Now, I like to install edgeR (http://toolshed.g2.bx.psu.edu/repository?repository_id=0c447003da85ae19) from the toolshed for further analyses. I cannot find a way to install that tool in my cloudman instance. My background is in psychiatry and I do not have any knowledge of Linux commands. Is there a way to install a tool (edgeR) from the toolshed without using command lines? Any help is greatly appreciated. Thank you. Best wishes, Anto Anto Rajkumar, MD, DNB, MRCPsych, PhD fellow, Department of Biomedicine, Aarhus university, 8000 C, Aarhus, Denmark. Ph (office) : 045- 87167292 E-mail: APR@hum-gen.au.dk<mailto:APR@hum-gen.au.dk> ___________________________________________________________ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
You've found a bug! I see what's going on -- it looks like the validation code doesn't understand email addresses with dashes ("hum-gen", your domain). I'll fix this, but for now you can always just register another user to use as admin "admin@cloudgalaxy.org" or whatever username you'd like. Register this user in galaxy, add it in that box, and you should be good to go. Thanks for noticing this! Dannon On Fri, Aug 16, 2013 at 10:29 AM, Anto Praveen Rajkumar Rajamani < APR@hum-gen.au.dk> wrote:
Hi Dannon,
Thank you for the kind reply. I see this error, while I have "registeredemailaddress@ec2domain.com" in the box. My registered email address is APR@hum-gen.au.dk. I use the domain name from my aws ec2 instance. Where do I go wrong?
Best wishes, Anto
Anto Rajkumar, MD, DNB, MRCPsych, PhD fellow, Department of Biomedicine, Aarhus university, 8000 C, Aarhus, Denmark. E-mail: APR@hum-gen.au.dk ------------------------------ *From:* Dannon Baker [dannon.baker@gmail.com] *Sent:* 16 August 2013 15:53
*To:* Anto Praveen Rajkumar Rajamani *Cc:* galaxy-dev@bx.psu.edu *Subject:* Re: [galaxy-dev] Is there a way to install a tool from toolshed in cloudman without using commands?
The only way I'm able to reproduce this on my end is by clicking "Add admin users" with the box next to it completely empty:
[image: Inline image 1]
You're seeing this error, and you have 'yourname@domain.com' in the box?
On Fri, Aug 16, 2013 at 9:14 AM, Anto Praveen Rajkumar Rajamani < APR@hum-gen.au.dk> wrote:
Hi Dannon,
I visited admin panel of http://<my_ec2_instance>/cloud/admin Under Add Galaxy admin users, I typed my email and pushed the "Add admin users" tab. I get the following message, Either no acceptable admin values provided ([]) or Galaxy service not found Current Galaxy admin remains as cloud@galaxyproject.org. Where do I go wrong? How do I create the new admin user?
Best wishes, Anto
------------------------------ *From:* Dannon Baker [dannon.baker@gmail.com] *Sent:* 16 August 2013 14:04 *To:* Anto Praveen Rajkumar Rajamani *Cc:* galaxy-dev@bx.psu.edu *Subject:* Re: [galaxy-dev] Is there a way to install a tool from toolshed in cloudman without using commands?
Hi Anto,
Yes, you should be able to create an admin user for your galaxy installation via the cloudman admin panel (http://<your_ec2_instance>/cloud/admin) in as an admin. Once you're an admin user, you'll see the toolshed installation stuff in the galaxy admin panel.
-Dannon
On Fri, Aug 16, 2013 at 6:03 AM, Anto Praveen Rajkumar Rajamani < APR@hum-gen.au.dk> wrote:
Hello,
I launched a new Cloudman instance last week to analyse my RNA-seq data. I uploaded and cleaned my data, but could not run Tophat and Cufflinks due to the "Broken symbolic links" problem ( https://bitbucket.org/galaxy/cloudman/issue/6/tool-default-symbolic-links-to... ). I have completed running Tophat2 on the public server. Now, I like to install edgeR ( http://toolshed.g2.bx.psu.edu/repository?repository_id=0c447003da85ae19) from the toolshed for further analyses. I cannot find a way to install that tool in my cloudman instance. My background is in psychiatry and I do not have any knowledge of Linux commands. Is there a way to install a tool (edgeR) from the toolshed without using command lines? Any help is greatly appreciated. Thank you.
Best wishes, Anto
Anto Rajkumar, MD, DNB, MRCPsych, PhD fellow, Department of Biomedicine, Aarhus university, 8000 C, Aarhus, Denmark. Ph (office) : 045- 87167292 E-mail: APR@hum-gen.au.dk
___________________________________________________________ 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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Dannon, I will try with my yahoo id (does not have the dash) and will write to you soon. Thank you. Best wishes, Anto Anto Rajkumar, MD, DNB, MRCPsych, PhD fellow, Department of Biomedicine, Aarhus university, 8000 C, Aarhus, Denmark. Ph (office) : 045- 87167292 E-mail: APR@hum-gen.au.dk ________________________________ From: Dannon Baker [dannon.baker@gmail.com] Sent: 16 August 2013 16:33 To: Anto Praveen Rajkumar Rajamani Cc: galaxy-dev@bx.psu.edu Subject: Re: [galaxy-dev] Is there a way to install a tool from toolshed in cloudman without using commands? You've found a bug! I see what's going on -- it looks like the validation code doesn't understand email addresses with dashes ("hum-gen", your domain). I'll fix this, but for now you can always just register another user to use as admin "admin@cloudgalaxy.org<mailto:admin@cloudgalaxy.org>" or whatever username you'd like. Register this user in galaxy, add it in that box, and you should be good to go. Thanks for noticing this! Dannon On Fri, Aug 16, 2013 at 10:29 AM, Anto Praveen Rajkumar Rajamani <APR@hum-gen.au.dk<mailto:APR@hum-gen.au.dk>> wrote: Hi Dannon, Thank you for the kind reply. I see this error, while I have "registeredemailaddress@ec2domain.com<mailto:registeredemailaddress@ec2domain.com>" in the box. My registered email address is APR@hum-gen.au.dk<mailto:APR@hum-gen.au.dk>. I use the domain name from my aws ec2 instance. Where do I go wrong? Best wishes, Anto Anto Rajkumar, MD, DNB, MRCPsych, PhD fellow, Department of Biomedicine, Aarhus university, 8000 C, Aarhus, Denmark. E-mail: APR@hum-gen.au.dk<mailto:APR@hum-gen.au.dk> ________________________________ From: Dannon Baker [dannon.baker@gmail.com<mailto:dannon.baker@gmail.com>] Sent: 16 August 2013 15:53 To: Anto Praveen Rajkumar Rajamani Cc: galaxy-dev@bx.psu.edu<mailto:galaxy-dev@bx.psu.edu> Subject: Re: [galaxy-dev] Is there a way to install a tool from toolshed in cloudman without using commands? The only way I'm able to reproduce this on my end is by clicking "Add admin users" with the box next to it completely empty: [Inline image 1] You're seeing this error, and you have 'yourname@domain.com<mailto:yourname@domain.com>' in the box? On Fri, Aug 16, 2013 at 9:14 AM, Anto Praveen Rajkumar Rajamani <APR@hum-gen.au.dk<mailto:APR@hum-gen.au.dk>> wrote: Hi Dannon, I visited admin panel of http://<my_ec2_instance>/cloud/admin Under Add Galaxy admin users, I typed my email and pushed the "Add admin users" tab. I get the following message, Either no acceptable admin values provided ([]) or Galaxy service not found Current Galaxy admin remains as cloud@galaxyproject.org<mailto:cloud@galaxyproject.org>. Where do I go wrong? How do I create the new admin user? Best wishes, Anto ________________________________ From: Dannon Baker [dannon.baker@gmail.com<mailto:dannon.baker@gmail.com>] Sent: 16 August 2013 14:04 To: Anto Praveen Rajkumar Rajamani Cc: galaxy-dev@bx.psu.edu<mailto:galaxy-dev@bx.psu.edu> Subject: Re: [galaxy-dev] Is there a way to install a tool from toolshed in cloudman without using commands? Hi Anto, Yes, you should be able to create an admin user for your galaxy installation via the cloudman admin panel (http://<your_ec2_instance>/cloud/admin) in as an admin. Once you're an admin user, you'll see the toolshed installation stuff in the galaxy admin panel. -Dannon On Fri, Aug 16, 2013 at 6:03 AM, Anto Praveen Rajkumar Rajamani <APR@hum-gen.au.dk<mailto:APR@hum-gen.au.dk>> wrote: Hello, I launched a new Cloudman instance last week to analyse my RNA-seq data. I uploaded and cleaned my data, but could not run Tophat and Cufflinks due to the "Broken symbolic links" problem (https://bitbucket.org/galaxy/cloudman/issue/6/tool-default-symbolic-links-to...). I have completed running Tophat2 on the public server. Now, I like to install edgeR (http://toolshed.g2.bx.psu.edu/repository?repository_id=0c447003da85ae19) from the toolshed for further analyses. I cannot find a way to install that tool in my cloudman instance. My background is in psychiatry and I do not have any knowledge of Linux commands. Is there a way to install a tool (edgeR) from the toolshed without using command lines? Any help is greatly appreciated. Thank you. Best wishes, Anto Anto Rajkumar, MD, DNB, MRCPsych, PhD fellow, Department of Biomedicine, Aarhus university, 8000 C, Aarhus, Denmark. Ph (office) : 045- 87167292 E-mail: APR@hum-gen.au.dk<mailto:APR@hum-gen.au.dk> ___________________________________________________________ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Dannon, As you suggested, I added me as an admin in my cloudman, using one of my email without the "-" in between. I could install edgeR package from the toolshed. However, the installed package failed to run with the message, error An error occurred with this dataset: sh: 1: htseq-count: not found sh: 1: htseq-count: not found sh: 1: htseq-count: not found sh: 1: htseq-count: not found Is this a problem with the tool, or with my installation, or with the "Broken symlink" ? Thank you. Best wishes, Anto
participants (2)
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Anto Praveen Rajkumar Rajamani -
Dannon Baker