Re: [galaxy-dev] Problem Running TopHat2

2014-09-01 Thread Kevin 
Hi Alper,
I think that the problem is somewhat fixed now. After I moved the samtools 
executable into the TopHat2 /bin, I also went into the “universe_wsgi.ini” and 
uncommented+changed the line “retry_metadata_internally=true” to 
“retry_metadata_internally=false”.
Then, when I ran the TopHat2 alignment again, the job was able to be completed. 
However, now the only problem is a small notification under the accepted hits 
file saying that “An error occurred setting the metadata for this dataset. You 
may be able to set it manually or retry auto-detection”
Is the metadata something I should be concerned about? Or is it okay to proceed 
without the metadata being completely done? I intend to use this accepted hits 
file for Cufflinks and Cuffdiff later on.
Thanks for all your help,
Kevin Chang
Sent: ‎Friday‎, ‎August‎ ‎29‎, ‎2014 ‎10‎:‎52‎ ‎AM
To: Kevin
Cc: galaxy-dev@lists.bx.psu.edu
Kevin,
You should install samtools to your operating system and put the executable 
file to your /usr/local/bin or somewhere in a path that galaxy user can call.
Best,
Alper
From: Kevin <chang...@byramhills.net>
Date: Friday, August 29, 2014 at 10:44 AM
To: Alper Kucukural <al...@kucukural.com>
Cc: "galaxy-dev@lists.bx.psu.edu" 
<galaxy-dev@lists.bx.psu.edu>
Subject: Re: [galaxy-dev] Problem Running TopHat2
The error message was the same thing as before:
Traceback (most recent call last):
File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in 
queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in finish
dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta 
directly for the initial set_meta call during dataset creation
File "/home/ubuntu/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, in 
set_meta
raise Exception, "Error Setting BAM Metadata: %s" % stderr
Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found
Thanks,
Kevin Chang
From: Alper Kucukural
Sent: Friday, August 29, 2014 10:16 AM
To: Kevin
Cc: galaxy-dev@lists.bx.psu.edu
What was the error?
From: Kevin <chang...@byramhills.net>
Date: Thursday, August 28, 2014 at 11:17 PM
To: Alper Kucukural <al...@kucukural.com>
Cc: "galaxy-dev@lists.bx.psu.edu" 
<galaxy-dev@lists.bx.psu.edu>
Subject: Re: [galaxy-dev] Problem Running TopHat2
Hi Alper,
Thank you for the advice. After you suggested that I install the samtools and 
not just the samtools binary, I went to the Galaxy Main Tool Shed and installed 
the “package_samtools_0_1_18”. After running TopHat2 again for around 36 hours, 
the same error message came up again. It appears that installing the samtools 
themselves did not fix the problem.
Are there any other ways to try and fix this problem?
Thanks for taking the time to help me out,
Kevin Chang
Sent from Windows Mail
From: Alper Kucukural
Sent: Tuesday, August 26, 2014 1:21 PM
To: Kevin
Cc: galaxy-dev@lists.bx.psu.edu
Hey Kevin,
You need to install samtools and bowtie(2) into your system. I assume, the 
package you installed to galaxy is just a wrapper to call samtools. It doesn’t 
come with samtools binary.
Best,
Alper Kucukural, PhD
Bioinformatics Core,
University of Massachusetts Medical School
368 Plantation St.Room AS4.2067
Worcester, MA 01605-2324
Phone: 774-312-4493
E-mail: alper.kucuku...@umassmed.edu
On Aug 26, 2014, at 11:36 AM, Kevin 
<chang...@byramhills.net> wrote:
Hello All,
I am running a Galaxy instance on Linux and have installed tools from the 
Galaxy Main Tool Shed. However, whenever I run TopHat2, the program is unable 
to complete the job before I get the following error message:
Traceback (most recent call last):
File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in 
queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in finish
dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta 
directly for the initial set_meta call during dataset creation
File "/home/ubuntu/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, in 
set_meta
raise Exception, "Error Setting BAM Metadata: %s" % stderr
Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found
So far, I have made sure that the samtools do appear to be installed since they 
can be found listed under "Managed Installed Tool Shed Repositories". Is it 
possible that they were installed incorrectly?
Any help is much appreciated.
Thanks for taking the time to read this,
Kevin Chang
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Re: [galaxy-dev] Problem Running TopHat2

2014-09-01 Thread Kevin 
The error message was the same thing as before:
Traceback (most recent call last):
File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in 
queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in finish
dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta 
directly for the initial set_meta call during dataset creation
File "/home/ubuntu/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, in 
set_meta
raise Exception, "Error Setting BAM Metadata: %s" % stderr
Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found
Thanks,
Kevin Chang
From: Alper Kucukural
Sent: ‎Friday‎, ‎August‎ ‎29‎, ‎2014 ‎10‎:‎16‎ ‎AM
To: Kevin
Cc: galaxy-dev@lists.bx.psu.edu
What was the error?
From: Kevin <chang...@byramhills.net>
Date: Thursday, August 28, 2014 at 11:17 PM
To: Alper Kucukural <al...@kucukural.com>
Cc: "galaxy-dev@lists.bx.psu.edu" 
<galaxy-dev@lists.bx.psu.edu>
Subject: Re: [galaxy-dev] Problem Running TopHat2
Hi Alper,
Thank you for the advice. After you suggested that I install the samtools and 
not just the samtools binary, I went to the Galaxy Main Tool Shed and installed 
the “package_samtools_0_1_18”. After running TopHat2 again for around 36 hours, 
the same error message came up again. It appears that installing the samtools 
themselves did not fix the problem.
Are there any other ways to try and fix this problem?
Thanks for taking the time to help me out,
Kevin Chang
Sent from Windows Mail
From: Alper Kucukural
Sent: Tuesday, August 26, 2014 1:21 PM
To: Kevin
Cc: galaxy-dev@lists.bx.psu.edu
Hey Kevin,
You need to install samtools and bowtie(2) into your system. I assume, the 
package you installed to galaxy is just a wrapper to call samtools. It doesn’t 
come with samtools binary.
Best,
Alper Kucukural, PhD
Bioinformatics Core,
University of Massachusetts Medical School
368 Plantation St.Room AS4.2067
Worcester, MA 01605-2324
Phone: 774-312-4493
E-mail: alper.kucuku...@umassmed.edu
On Aug 26, 2014, at 11:36 AM, Kevin 
<chang...@byramhills.net> wrote:
Hello All,
I am running a Galaxy instance on Linux and have installed tools from the 
Galaxy Main Tool Shed. However, whenever I run TopHat2, the program is unable 
to complete the job before I get the following error message:
Traceback (most recent call last):
File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in 
queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in finish
dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta 
directly for the initial set_meta call during dataset creation
File "/home/ubuntu/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, in 
set_meta
raise Exception, "Error Setting BAM Metadata: %s" % stderr
Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found
So far, I have made sure that the samtools do appear to be installed since they 
can be found listed under "Managed Installed Tool Shed Repositories". Is it 
possible that they were installed incorrectly?
Any help is much appreciated.
Thanks for taking the time to read this,
Kevin Chang
___
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Re: [galaxy-dev] Problem Running TopHat2

2014-09-01 Thread Kevin 
Hi Alper,
Thank you for the advice. After you suggested that I install the samtools and 
not just the samtools binary, I went to the Galaxy Main Tool Shed and installed 
the “package_samtools_0_1_18”. After running TopHat2 again for around 36 hours, 
the same error message came up again. It appears that installing the samtools 
themselves did not fix the problem.
Are there any other ways to try and fix this problem?
Thanks for taking the time to help me out,
Kevin Chang
Sent from Windows Mail
From: Alper Kucukural
Sent: ‎Tuesday‎, ‎August‎ ‎26‎, ‎2014 ‎1‎:‎21‎ ‎PM
To: Kevin
Cc: galaxy-dev@lists.bx.psu.edu
Hey Kevin,
You need to install samtools and bowtie(2) into your system. I assume, the 
package you installed to galaxy is just a wrapper to call samtools. It doesn’t 
come with samtools binary.
Best,
Alper Kucukural, PhD
Bioinformatics Core,
University of Massachusetts Medical School
368 Plantation St.Room AS4.2067
Worcester, MA 01605-2324
Phone: 774-312-4493
E-mail: alper.kucuku...@umassmed.edu
On Aug 26, 2014, at 11:36 AM, Kevin 
 wrote:
Hello All,
I am running a Galaxy instance on Linux and have installed tools from the 
Galaxy Main Tool Shed. However, whenever I run TopHat2, the program is unable 
to complete the job before I get the following error message:
Traceback (most recent call last):
File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in 
queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in finish
dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta 
directly for the initial set_meta call during dataset creation
File "/home/ubuntu/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, in 
set_meta
raise Exception, "Error Setting BAM Metadata: %s" % stderr
Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found
So far, I have made sure that the samtools do appear to be installed since they 
can be found listed under "Managed Installed Tool Shed Repositories". Is it 
possible that they were installed incorrectly?
Any help is much appreciated.
Thanks for taking the time to read this,
Kevin Chang
___
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in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] Problem Running TopHat2

2014-08-29 Thread Alper Kucukural 
Kevin,
You should install samtools to your operating system and put the executable
file to your /usr/local/bin or somewhere in a path that galaxy user can
call. 
Best,
Alper

From:  Kevin 
Date:  Friday, August 29, 2014 at 10:44 AM
To:  Alper Kucukural 
Cc:  "galaxy-dev@lists.bx.psu.edu" 
Subject:  Re: [galaxy-dev] Problem Running TopHat2

The error message was the same thing as before:

Traceback (most recent call last):
  File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/runners/local.py", line
129, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
  File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in
finish
dataset.datatype.set_meta( dataset, overwrite=False )  # call
datatype.set_meta directly for the initial set_meta call during dataset
creation
  File "/home/ubuntu/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251,
in set_meta
raise Exception, "Error Setting BAM Metadata: %s" % stderr
Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found

Thanks,
Kevin Chang

From: Alper Kucukural <mailto:al...@kucukural.com>
Sent: Friday, August 29, 2014 10:16 AM
To: Kevin <mailto:chang...@byramhills.net>
Cc: galaxy-dev@lists.bx.psu.edu

What was the error?

From:  Kevin 
Date:  Thursday, August 28, 2014 at 11:17 PM
To:  Alper Kucukural 
Cc:  "galaxy-dev@lists.bx.psu.edu" 
Subject:  Re: [galaxy-dev] Problem Running TopHat2

Hi Alper,

Thank you for the advice. After you suggested that I install the samtools
and not just the samtools binary, I went to the Galaxy Main Tool Shed and
installed the ³package_samtools_0_1_18². After running TopHat2 again for
around 36 hours, the same error message came up again. It appears that
installing the samtools themselves did not fix the problem.

Are there any other ways to try and fix this problem?

Thanks for taking the time to help me out,
Kevin Chang


Sent from Windows Mail

From: Alper Kucukural <mailto:al...@kucukural.com>
Sent: Tuesday, August 26, 2014 1:21 PM
To: Kevin <mailto:chang...@byramhills.net>
Cc: galaxy-dev@lists.bx.psu.edu

Hey Kevin, 
You need to install samtools and bowtie(2) into your system. I assume, the
package you installed to galaxy is just a wrapper to call samtools. It
doesn¹t come with samtools binary.
Best,
Alper Kucukural, PhD
Bioinformatics Core,
University of Massachusetts Medical School
368 Plantation St.Room AS4.2067
Worcester, MA 01605-2324
Phone: 774-312-4493
E-mail: alper.kucuku...@umassmed.edu



On Aug 26, 2014, at 11:36 AM, Kevin  wrote:

> Hello All,
> 
> 
> I am running a Galaxy instance on Linux and have installed tools from the
> Galaxy Main Tool Shed. However, whenever I run TopHat2, the program is unable
> to complete the job before I get the following error message:
> 
> Traceback (most recent call last):
>   File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129,
> in queue_job
> job_wrapper.finish( stdout, stderr, exit_code )
>   File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in
> finish
> dataset.datatype.set_meta( dataset, overwrite=False )  # call
> datatype.set_meta directly for the initial set_meta call during dataset
> creation
>   File "/home/ubuntu/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, in
> set_meta
> raise Exception, "Error Setting BAM Metadata: %s" % stderr
> Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found
> 
> So far, I have made sure that the samtools do appear to be installed since
> they can be found listed under "Managed Installed Tool Shed Repositories". Is
> it possible that they were installed incorrectly?
> Any help is much appreciated.
> 
> 
> Thanks for taking the time to read this,
> Kevin Chang
> 
> 
> ___
> 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/







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Re: [galaxy-dev] Problem Running TopHat2

2014-08-29 Thread Alper Kucukural 
What was the error?

From:  Kevin 
Date:  Thursday, August 28, 2014 at 11:17 PM
To:  Alper Kucukural 
Cc:  "galaxy-dev@lists.bx.psu.edu" 
Subject:  Re: [galaxy-dev] Problem Running TopHat2

Hi Alper,

Thank you for the advice. After you suggested that I install the samtools
and not just the samtools binary, I went to the Galaxy Main Tool Shed and
installed the ³package_samtools_0_1_18². After running TopHat2 again for
around 36 hours, the same error message came up again. It appears that
installing the samtools themselves did not fix the problem.

Are there any other ways to try and fix this problem?

Thanks for taking the time to help me out,
Kevin Chang


Sent from Windows Mail

From: Alper Kucukural <mailto:al...@kucukural.com>
Sent: Tuesday, August 26, 2014 1:21 PM
To: Kevin <mailto:chang...@byramhills.net>
Cc: galaxy-dev@lists.bx.psu.edu

Hey Kevin, 
You need to install samtools and bowtie(2) into your system. I assume, the
package you installed to galaxy is just a wrapper to call samtools. It
doesn¹t come with samtools binary.
Best,
Alper Kucukural, PhD
Bioinformatics Core,
University of Massachusetts Medical School
368 Plantation St.Room AS4.2067
Worcester, MA 01605-2324
Phone: 774-312-4493
E-mail: alper.kucuku...@umassmed.edu



On Aug 26, 2014, at 11:36 AM, Kevin  wrote:

> Hello All,
> 
> 
> I am running a Galaxy instance on Linux and have installed tools from the
> Galaxy Main Tool Shed. However, whenever I run TopHat2, the program is unable
> to complete the job before I get the following error message:
> 
> Traceback (most recent call last):
>   File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129,
> in queue_job
> job_wrapper.finish( stdout, stderr, exit_code )
>   File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in
> finish
> dataset.datatype.set_meta( dataset, overwrite=False )  # call
> datatype.set_meta directly for the initial set_meta call during dataset
> creation
>   File "/home/ubuntu/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, in
> set_meta
> raise Exception, "Error Setting BAM Metadata: %s" % stderr
> Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found
> 
> So far, I have made sure that the samtools do appear to be installed since
> they can be found listed under "Managed Installed Tool Shed Repositories". Is
> it possible that they were installed incorrectly?
> Any help is much appreciated.
> 
> 
> Thanks for taking the time to read this,
> Kevin Chang
> 
> 
> ___
> 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/





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Please keep all replies on the list by using "reply all"
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Re: [galaxy-dev] Problem Running TopHat2

2014-08-26 Thread Alper Kucukural 
Hey Kevin, 
You need to install samtools and bowtie(2) into your system. I assume, the 
package you installed to galaxy is just a wrapper to call samtools. It doesn’t 
come with samtools binary.
Best,
Alper Kucukural, PhD
Bioinformatics Core,
University of Massachusetts Medical School
368 Plantation St.Room AS4.2067
Worcester, MA 01605-2324
Phone: 774-312-4493
E-mail: alper.kucuku...@umassmed.edu



On Aug 26, 2014, at 11:36 AM, Kevin  wrote:

> Hello All,
> 
> 
> I am running a Galaxy instance on Linux and have installed tools from the 
> Galaxy Main Tool Shed. However, whenever I run TopHat2, the program is unable 
> to complete the job before I get the following error message:
> 
> Traceback (most recent call last):
> 
> 
>   File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, 
> in queue_job
> 
> 
> job_wrapper.finish( stdout, stderr, exit_code )
> 
> 
>   File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in 
> finish
> 
> 
> dataset.datatype.set_meta( dataset, overwrite=False )  # call 
> datatype.set_meta directly for the initial set_meta call during dataset 
> creation
> 
> 
>   File "/home/ubuntu/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, 
> in set_meta
> 
> 
> raise Exception, "Error Setting BAM Metadata: %s" % stderr
> 
> 
> Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found
> 
> So far, I have made sure that the samtools do appear to be installed since 
> they can be found listed under "Managed Installed Tool Shed Repositories". Is 
> it possible that they were installed incorrectly?
> Any help is much appreciated.
> 
> 
> Thanks for taking the time to read this,
> Kevin Chang
> 
> 
> ___
> 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/

___
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[galaxy-dev] Problem Running TopHat2

2014-08-26 Thread Kevin 
Hello All,
I am running a Galaxy instance on Linux and have installed tools from the 
Galaxy Main Tool Shed. However, whenever I run TopHat2, the program is unable 
to complete the job before I get the following error message:
Traceback (most recent call last):
File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129, in 
queue_job
job_wrapper.finish( stdout, stderr, exit_code )
File "/home/ubuntu/galaxy-dist/lib/galaxy/jobs/__init__.py", line 998, in finish
dataset.datatype.set_meta( dataset, overwrite=False ) # call datatype.set_meta 
directly for the initial set_meta call during dataset creation
File "/home/ubuntu/galaxy-dist/lib/galaxy/datatypes/binary.py", line 251, in 
set_meta
raise Exception, "Error Setting BAM Metadata: %s" % stderr
Exception: Error Setting BAM Metadata: /bin/sh: 1: samtools: not found
So far, I have made sure that the samtools do appear to be installed since they 
can be found listed under "Managed Installed Tool Shed Repositories". Is it 
possible that they were installed incorrectly?
Any help is much appreciated.
Thanks for taking the time to read this,
Kevin Chang

___
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:
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