Dear Galaxy Developers,
I would like to have this tool integrated into Galaxy. It is similar to
SignalP, however, where SignalP predict conventional secretion /
membrane integration, SecretomeP predicts unconventional secretion. More
information is in the attached paper.
A browser-version of Secr
Hi Bob,
I'd suggest you to open an issue at
https://github.com/galaxyproject/galaxy/issues/new
Cheers,
Nicola
On 12/11/15 16:29, rbrown1...@comcast.net wrote:
Good morning Team,
Could you please fix the "Run workflow" button that does NOT gray-out
when clicked? This causes my users to doub
On Thu, Nov 12, 2015 at 4:24 PM, Olivier CLAUDE wrote:
> I followed the instuctions given by peter and signalp works with galaxy!
> Thanks a lot!
> Do I try the same for tmhmm2 and promoter2?
> Thanks a lot again!
>
> Olivier
Our notes from installing tmhmm2:
TMHMM arrives as the compressed file
I followed the instuctions given by peter and signalp works with galaxy!
Thanks a lot!
Do I try the same for tmhmm2 and promoter2?
Thanks a lot again!
Olivier
-Message d'origine-
De : Peter Cock [mailto:p.j.a.c...@googlemail.com]
Envoyé : jeudi 12 novembre 2015 16:36
À : Björn Grüning
On Thu, Nov 12, 2015 at 2:56 PM, Björn Grüning
wrote:
> Hi,
>
> please make also sure the /bin directory inside of the signalp folder is
> in your PATH.
>
> Things like combine-hmm-plp.awk should be included.
>
> Ciao,
> Bjoern
Thanks Bjorn,
You don't need put that on the path, alternatively you
Is gnuplot installed?
Am 12.11.2015 um 16:23 schrieb Olivier CLAUDE:
> Hello again,
>
> I have put the /signalp-3.0/bin in the path and it changed the error message
> to :
> "error running /usr/bin/gnuplot on
> /signal-3.0/tmp/TMP1531945/plot.gnu"
>
> I have restarted galaxy tried the same
Hello again,
I have put the /signalp-3.0/bin in the path and it changed the error message to
:
"error running /usr/bin/gnuplot on
/signal-3.0/tmp/TMP1531945/plot.gnu"
I have restarted galaxy tried the same search, no changes in the output.
Any idea for tmhmm also?
-Message d'origin
Hi, Ryan
Galaxy displays tabular data in the browser using a tag. It *sounds
like* the behavior you see (columns losing space between one another when
narrowing the window and getting more space as you expand the window) would
reflect that.
Carl
On Wed, Oct 28, 2015 at 1:23 PM, Ryan G wrote:
Hi Mic,
you can always dive into a container and get access to everything.
Please read about `docker exec`, also described in our readme file.
cheers,
Bjoern
Am 12.11.2015 um 15:24 schrieb Mic:
> HI Bjoern,
> Thank you for your email. I have just started to build a new docker
> container based o
Hi,
please make also sure the /bin directory inside of the signalp folder is
in your PATH.
Things like combine-hmm-plp.awk should be included.
Ciao,
Bjoern
Am 12.11.2015 um 15:14 schrieb Olivier CLAUDE:
> Hi Peter,
>
> I totally agree with you about the CBS, i had so much problems to get the
On Thu, Nov 12, 2015 at 2:14 PM, Olivier CLAUDE wrote:
> Hi Peter,
>
> I totally agree with you about the CBS, i had so much problems to get the
> files, there are so many restrictions with my university mails.
>
> ...
> My email editor changed "signalp" in"Signalp" and in"signal" in my previous
HI Bjoern,
Thank you for your email. I have just started to build a new docker
container based on bgruening/galaxy-stable:15.07 . It seems that 15.10 has
not been yet included.
The problem which I have with Docker container is that if a tool from the
toolshed failed to install then I can not get a
Hi Peter,
I totally agree with you about the CBS, i had so much problems to get the
files, there are so many restrictions with my university mails.
> That's not right - the case is all inconsistent. The binary name signalp is
> all lower case, so if gawk, but I infer you had something like this
Hi Olivier,
On Thu, Nov 12, 2015 at 1:03 PM, Olivier CLAUDE wrote:
> Hi Björn!
>
> I do have signalP 3 , it's installed and on the path.
Good. It is a shame that CBS use a proprietary license which forbids
redistribution and packaging - otherwise I could have tried to automate
this.
> The tests
Hi Björn!
I do have signalP 3 , it's installed and on the path.
The tests files are the ones from the archive (no changes nor I tried to open
it manually)
The exact lines in the prompt are:
$SIGNALP
Signalp -G -t euk test/test.seq
Gawk: fatal: cannot open file 'test/test.seq' for reading (no
Hi Olivier,
you need to have signalp in version 3.
You have installed it already and it is now on your $PATH?
> Signal P: with v3.0: it can’t localize it (signal not found) (I can’t even
> launch it in command line)
What is the error if you run it on command line?
Ciao,
Bjoern
>
>
Hi Mic,
Am 12.11.2015 um 01:22 schrieb Mic:
> Hello,
> I installed all tools from the toolshed which I needed for Galaxy (15.10)
> and noticed that I can not upload bigger files than 2 GB to Galaxy without
> a FTP server.
>
> I installed on Ubuntu 14.04 ProFTPD in the following way:
>
> *sud
Hello,
I am installing this package from peterjc.
I downloaded the tools from the CBS but i can’t run it in galaxy :
TMHMM : galaxy gives the error : no output from tmhmm2
Signal P: with v3.0: it can’t localize it (signal not found) (I can’t even
launch it in command line)
Hi all,
Thank you for the link. I did not know about the link.
@Bjoern: Few month back I saw somewhere a website where it was possible to
download a VM with Galaxy. By any chance, do you remember the link?
Thank you in advance.
Mic
On Wed, Nov 11, 2015 at 10:29 PM, Björn Grüning
wrote:
> Hi M
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