Ian,

To assist tracking down this issue, could you provide the output of the following commands?

uname -m uname -s

--Dave B.

On 12/20/2013 08:43 AM, UMD Bioinformatics wrote:

Hello Devteam,

I’ve just updated my local instance to the latest version. With the migration of tools to the tool shed I used the migrate command to keep my tools as they were in the previous versions.

$ sh ./scripts/migrate_tools/0008_tools.sh install_dependencies

and I’ve updated the database to 117

$ sh manage_db.sh upgrade

However, when I’m using samtools I’m getting an error related to the data. I’m not sure what the issue is and I’ve check all the .loc and .sh files and everything is pointing to the proper locations. Any ideas what the issue might be?

An error occurred with this dataset:Could not determine Samtools version /bin/sh: line 1: 1616 Segmentation fault: 11 samtools 2>&1 Error extracting alignments from (/galaxy-dist/database/files/001/dataset_1585.dat),

Cheers Ian

---

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Dave,

I’ve just decide to uninstall all the samtools and reinstall them. Things are working for now. Not sure what went wrong with the migration but seems to be back up and running.

Cheers Ian

On Dec 20, 2013, at 8:55 AM, Dave Bouvier dave@bx.psu.edu wrote:

Ian,

To assist tracking down this issue, could you provide the output of the following commands?

uname -m uname -s

--Dave B.

On 12/20/2013 08:43 AM, UMD Bioinformatics wrote:

...

Hello Devteam,

I’ve just updated my local instance to the latest version. With the migration of tools to the tool shed I used the migrate command to keep my tools as they were in the previous versions.

$ sh ./scripts/migrate_tools/0008_tools.sh install_dependencies

and I’ve updated the database to 117

$ sh manage_db.sh upgrade

However, when I’m using samtools I’m getting an error related to the data. I’m not sure what the issue is and I’ve check all the .loc and .sh files and everything is pointing to the proper locations. Any ideas what the issue might be?

An error occurred with this dataset:Could not determine Samtools version /bin/sh: line 1: 1616 Segmentation fault: 11 samtools 2>&1 Error extracting alignments from (/galaxy-dist/database/files/001/dataset_1585.dat),

Cheers Ian

---

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/