Hi all,
after an update to the following changeset(14859:7ba05957588a, stable,
05.12.14), our bam files that are uploaded(linked) to a data library, are
no longer indexed. The metadata_xxx.dat is created, but it stays empty.
The following error message appears in the log, although the state of the
you can run samtools from the command-line - can you do a which
> `samtools` from your command-line and see where it is coming from and
> then add that directory explicitly to your Galaxy PATH - say at the
> top of run.sh in your Galaxy root (let me know if you need more
> details on that)
great a reporting the nature of the problem.
>
> -John
>
> On Thu, Dec 18, 2014 at 7:51 AM, Jelle Scholtalbers
> wrote:
> > Hi John and others,
> >
> > The "OSError: [Errno 2] No such file or directory" is solved when putting
> > the "shel
Hi Teshome,
I assume you have good reasons for switching to LDAP (e.g. users only need
to remember their main password), but just as a side note, we recently
switched back from LDAP authentication to local user authentication to have
a bit more control. One of the main reasons is being able to 'im
Hi Björn, Eric, all,
I'm trying to get ipython running on our instance. Without the proxy, e.g.
http://myserver:8080 it works fine. However, with the proxy in front (e.g.
http://myserver/galaxy) I get this firefox error
"11:28:37.793 Cross-Origin Request Blocked: The Same Origin Policy
disallows r
Hi Jochen,
I recently took a probably more labour intensive approach.
# backup!
# mv prev-installation to somewhere else
# git clone to old-location
# git checkout -b master origin/master
# and copy over every config, tool xml, tool dependency directory,
tool-data loc files from the prev-installa
Hi all,
I have a related issue as I'm trying to set the format on discovered
datasets. Only setting e.g 'ext="fastqsanger"' seems to work. But the
following variations do not work to set a format, and similar to Alexander,
the history items do not show any datatype with these options.
Hi all,
On our installation (v15.07) we suddenly see that one of two job handlers
get stuck with a high cpu load (last message generally, `cleaning up
external metadata files`) without new messages appearing. In addition, when
running workflows in batch (>6x), only a few of them (~3) get their
wor
Hi Eric,
this is a script I have used in the past
https://github.com/scholtalbers/galaxy-test-workflows
It doesn't give you the nice feedback that you probably want, but maybe you
have some use for it anyway.
Cheers,
Jelle
On Wed, Dec 14, 2016 at 4:26 AM, Eric Rasche wrote:
> Wondering if an
Hi Jochen,
generally updating the database shouldn't be an issue as this is handled by
the migration scripts that incrementally update your db schema to match the
version.
But I would do a backup just in case.
For the outdated ini files you can use the tool called Meld to spot
differences between
Hi John,
as a tip, you can use the tool "ldapsearch", from e.g. the package
"openldap-client", to figure out with which attributes you search and which
attributes you can retrieve.
Examples:
$ ldapsearch -vv -x -H ldap://dc1.example.com -b cn=Users,dc=exampke,dc=org"
# retrieve all AD/ldap entrie
nv/lib/python2.7/site-packages/ldap/functions.py",
> line 135, in set_option
> return _ldap_function_call(None,_ldap.set_option,option,invalue)
> File
> "/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/ldap/functions.py",
> line 66, in _ldap_function_call
>
Hi all,
Again, this may be me sticking to old pre-tool shed habits - so I'd like
> to hear how other people manage their *.loc files, especially when doing
> hand editing to add entries.
>
I **try** to stick to just editing the *.loc file in tool-data for those
tools that do not have a data manag
Hi George,
on our instance I have noticed that the tmp (new_file_path) was taking up
quite some space and files were only deletable after restarting the web /
uwsgi process.
FYI a while ago I wrote this script which should ease the cronjob setup a
bit (does not cleanup tmp though):
https://github
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