Hello all,
This is resurrecting an old thread, but using $input.extra_files_path
rather than $input.files_path explained an unfortunate regression
in the BLAST+ wrappers reported earlier today:
https://github.com/peterjc/galaxy_blast/issues/69
Thanks John for his detective work. Given $output.fi
Thanks Peter for your very quick reply confirming that
workaround.
I'll wait to hear from John, as the real fix may be on the
Galaxy side, but we may need to push an update to the
Tool Shed to use the older .extra_files_path form in the
short term.
Thanks,
Peter
On Tue, Jul 21, 2015 at 7:22 PM,
Previous revision of ncbi_blast_plus works like a charm, thanks.
On 21 July 2015 at 19:57, Peter Cock wrote:
> Thanks Peter,
>
> Yes, you are using the latest release published to
> the Tool Shed, aka v0.1.03 (internal changes):
>
> https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/c16
Thanks Peter,
Yes, you are using the latest release published to
the Tool Shed, aka v0.1.03 (internal changes):
https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/c16c30e9ad5b
I've filed this as an issue on the GitHub repository,
https://github.com/peterjc/galaxy_blast/issues/69
If you
This is release_15.07 (last commit listed
is 39f6730e5f50b54f372b8c1e17d86d8936b5899f) and ncbi_blast_plus c16c30e9ad5b.
So no, its not an old Galaxy.
On 21 July 2015 at 17:37, Peter Cock wrote:
> Hi Peter v H,
>
> Which version of Galaxy are you running?
>
> Which version of ncbi_blast_tools ar
Yeah - that workflow run endpoint is fairly problematic since it
requires to workflow to be completely scheduled. There is code in
Galaxy and an API endpoint that will schedule the workflow in the
background - but bioblend hasn't been updated to use this yet. I've
created a bioblend issue to track
Apologies John - hit reply instead of reply-all first time around...
Maybe this is the right place to ask about the shed_tools and tool deps
directory permissions. Installing tools from the web I get a mixed bag of
folder permission, some at 775, some at 777
drwxrwxr-x 43 galaxy galaxy 4.0K Apr
Hello Peter,
Thanks a lot. It worked well. However the run stopped after a few minutes.
Here is the message :
Error aligning sequence. Error reading ebwt array: returned 113175904,
length was 823263360 Your index files may be corrupt; please try
re-building or re-downloading. A complete index consi
Hello,
i'm actually having a message of "connection reset by peer" when i'm launching
a long API request (upload files only links actually, run the workflow other
them and retrieve the results into a specific folder).
The workflow is working fine when i proceed to an analysis file by file but
Hi Peter v H,
Which version of Galaxy are you running?
Which version of ncbi_blast_tools are you running? (ideally down to
the ToolShed revision)
My guess is that since this used to be .extra_files_path perhaps your
Galaxy is too old for .files_path to work?
https://github.com/peterjc/galaxy_bla
Hi there
I'm trying to use the blastp tools from the ncbi_blast_tools, but every
time I try and run a job I get the following error:
Traceback (most recent call last):
File "/net/
datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/runners/__init__.py",
line 163, in pre
Hej Jelle,
I also thought of setting it up again from scratch...
@Marius I will check again the hg diff. The update with hg update worked
fine as far as I can see. So I'm not in a big hurry to change to git.
Cheers Jochen
On 21.07.2015 13:27, Jelle Scholtalbers wrote:
> Hi Jochen,
>
> I recent
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
Thanks Marius,
it does not look like it's working for me. There are to many changes in
git diff...
the git pull and cat local_changes.diff |patch -p1 -R gives me an
endless list of differences.
Cheers Jochen
On 21.07.2015 11:41, Marius van den Beek wrote:
> Hi Jochen,
>
> I recently did this.
Hi Jochen,
I recently did this. Instructions are here:
https://wiki.galaxyproject.org/Develop/SourceCode
This has worked for me:
(~/galaxy-dist is my production galaxy dir)
cd ~
git clone https://github.com/galaxyproject/galaxy.git
cd galaxy
git reset --hard 3f1cec451f6dadee52a70a14fc6f6899f7aacd
Hi,
is it possible to change from bitbucket to git? So I would like
future-update my galaxy from git instead from bitbucket.
Cheers Jochen
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