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.com Alper Kucukural Sent: ‎Tuesday‎, ‎August‎ ‎26‎, ‎2014 ‎1‎:‎21‎ ‎PM To:changk16@byramhills.net Kevin Cc:galaxy-dev@lists.bx.psu.edu 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.Kucukural@umassmed.edu Alper.Kucukural@umassmed.edu On Aug 26, 2014, at 11:36 AM, Kevin <changk16@byramhills.netchangk16@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 ___________________________________________________________ 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/http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/http://galaxyproject.org/search/mailinglists/

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.com Alper Kucukural Sent: ‎Friday‎, ‎August‎ ‎29‎, ‎2014 ‎10‎:‎16‎ ‎AM To:changk16@byramhills.net Kevin Cc:galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu What was the error? From: Kevin <changk16@byramhills.netchangk16@byramhills.net> Date: Thursday, August 28, 2014 at 11:17 PM To: Alper Kucukural <alper@kucukural.comalper@kucukural.com> Cc: "galaxy-dev@lists.bx.psu.edugalaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edugalaxy-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.com Alper Kucukural Sent: Tuesday, August 26, 2014 1:21 PM To:changk16@byramhills.net Kevin Cc:galaxy-dev@lists.bx.psu.edu 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.Kucukural@umassmed.edu Alper.Kucukural@umassmed.edu On Aug 26, 2014, at 11:36 AM, Kevin <changk16@byramhills.netchangk16@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 ___________________________________________________________ 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/http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/http://galaxyproject.org/search/mailinglists/

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:changk16@byramhills.net Kevin Cc:galaxy-dev@lists.bx.psu.edu 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 <changk16@byramhills.netchangk16@byramhills.net> Date: Friday, August 29, 2014 at 10:44 AM To: Alper Kucukural <alper@kucukural.comalper@kucukural.com> Cc: "galaxy-dev@lists.bx.psu.edugalaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edugalaxy-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.com Alper Kucukural Sent: Friday, August 29, 2014 10:16 AM To:changk16@byramhills.net Kevin Cc:galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu What was the error? From: Kevin <changk16@byramhills.netchangk16@byramhills.net> Date: Thursday, August 28, 2014 at 11:17 PM To: Alper Kucukural <alper@kucukural.comalper@kucukural.com> Cc: "galaxy-dev@lists.bx.psu.edugalaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edugalaxy-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.com Alper Kucukural Sent: Tuesday, August 26, 2014 1:21 PM To:changk16@byramhills.net Kevin Cc:galaxy-dev@lists.bx.psu.edu 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.Kucukural@umassmed.edu Alper.Kucukural@umassmed.edu On Aug 26, 2014, at 11:36 AM, Kevin <changk16@byramhills.netchangk16@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 ___________________________________________________________ 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/http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/http://galaxyproject.org/search/mailinglists/