Re: [galaxy-dev] IPython and Rstudio are missing

[Mic]

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 Mic,
>
> have a look at this page.
>
> https://galaxy.readthedocs.org/en/master/admin/interactive_environments.html
>
> Which version of Galaxy you are using?
> Cheers,
> Bjoern
>
> Am 11.11.2015 um 11:05 schrieb Mic:
> > Hi all,
> > Is there any log files which could show what did go wrong or is there any
> > documentation how to install IEs?
> >
> > Thank you in advance.
> >
> > Mic
> >
> > On Mon, Nov 9, 2015 at 9:12 AM, Mic  wrote:
> >
> >> Hi Bjoern,
> >> Thank you for your email. I tried the attached Annovar output which is
> >> tabular separated. Unfortunately, Rstudio and Ipython still did not
> show up.
> >>
> >> Thank you in advance.
> >>
> >> Best wishes,
> >>
> >> Mic
> >>
> >> On Sat, Nov 7, 2015 at 9:58 AM, Björn Grüning <
> bjoern.gruen...@gmail.com>
> >> wrote:
> >>
> >>> Hi Mic,
> >>>
> >>> please check any other file than a VCF file. Try a txt file for
> example.
> >>>
> >>> Thanks,
> >>> Bjoern
> >>>
> >>> Am 07.11.2015 um 00:54 schrieb Mic:
>  Hi Eric,
>  I added your line to ipython.xml and rstudio.xml and restarted Galaxy,
> >>> but
>  still Rstudio and Ipython do not appear on my test.vcf file by
> clicking
> >>> the
>  *visualize* icon.
> 
>    result_type="datatype">tabular.Tabular
>    result_type="datatype">data.Text
>  *  result_type="datatype">tabular.VCF*
> 
>  What did I miss?
> 
>  Thank you in advance.
> 
>  Mic
> 
>  On Sat, Nov 7, 2015 at 1:13 AM, Eric Rasche  wrote:
> 
> > Hi Mic,
> >
> > I don't believe GIEs are currently activated for anything other than
> >>> plain
> > text and tabular files. You can edit the
> >
> >>>
> $GALAXY_ROOT/config/plugins/interactive_environments/ipython/config/ipython.xml
> > (and rstudio/config/rstudio.xml) files to add a line like:
> >
> > Konsole output
> >  > result_type="datatype">tabular.VCF
> >
> > and that /should/ let you open VCF files. (I haven't tested that
> exact
> > datatype but I believe that should work). GIEs have been somewhat
> > experimental so far, so we haven't felt the need to expand which
> >>> datatypes
> > they apply to lest we overwhelm/surprise users.
> >
> > Ciao,
> > Eric
> >
> >
> >
> >
> > On 11/06/2015 02:56 AM, Mic wrote:
> >> Hello,
> >> Last week, I cloned Galaxy from Github. I uploaded a VCF file from
> my
> >> computer. I also installed the following additional software:
> >>
> >> /apt-key adv --keyserver keyserver.ubuntu.com
> >>  --recv-keys E084DAB9/
> >> /echo 'deb http://cran.r-project.org/bin/linux/ubuntu trusty/' >>
> >> /etc/apt/sources.list/
> >> /apt-get -qq update && apt-get install --no-install-recommends -y
> >> libcurl4-openssl-dev libxml2-dev/
> >> /apt-get install apt-transport-https python-dev libc-dev pandoc
> >> pkg-config liblzma-dev libbz2-dev libpcre3-dev/
> >> /apt-get install libblas-dev liblapack-dev gfortran libzmq3-dev
> curl/
> >> /apt-get install libfreetype6-dev libpng-dev net-tools procps r-base
> >> libreadline-dev /
> >> /pip install distribute --upgrade/
> >> /pip install scipy sklearn-pandas bioblend matplotlib patsy pysam
> >>> khmer
> >> ggplot mpld3 sympy rpy2/
> >> /pip install pyzmq ipython==2.4 jinja2 tornado pygments numpy
> >>> biopython
> >> scikit-learn pandas/
> >>
> >> However, clicking the /visualize/ icon no iPython and RStudio are
> >> visible. Galaxy is in my home folder installed
> //home/lorencm/galaxy./
> >>
> >> What am I missing?
> >>
> >> Thank you in advance.
> >>
> >> Mic
> >>
> >>
> >> ___
> >> 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:
> >>   https://lists.galaxyproject.org/
> >>
> >> To search Galaxy mailing lists use the unified search at:
> >>   http://galaxyproject.org/search/mailinglists/
> >>
> >
> > --
> > Eric Rasche
> > Programmer II
> >
> > Center for Phage Technology
> > Rm 312A, BioBio
> > Texas A University
> > College Station, TX 77843
> > 404-692-2048
> > e...@tamu.edu
> >
> >
> 
> 
> 
>  ___
>  Please keep all replies on the list by using "reply all"
>  in your mail 

Re: [galaxy-dev] ProFTPD with SQLite

[Björn Grüning]

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:
> 
> *sudo aptitude install ProFTPD proftpd-mod-sqlite sqlite3*
> 
> Unfortunately, I do not know how to connect the ProFTPD with Galaxy's
> SQLite.

ProFTP is an FTP Server and SQLite is a database you cannot connect from
the one the the other.

Are you still using the Galaxy Docker? If so we have already installed a
FTP Server for you and configured it so Galaxy can talk to the FTP server.

Please see the documentation about the Docker FTP server:
https://github.com/bgruening/docker-galaxy-stable

To transfer data from your client to Galaxy you only need an FTP cient.
Have a look at Filezilla as FTP-client.

Cheers,
Bjoern

> Thank you in advance.
> 
> Mic
> 
> 
> 
> ___
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Re: [galaxy-dev] Tmhmm and signal P

[Björn Grüning]

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

> 
> With v4.1 it can’t be reached by galaxy (I am thinking about 
> something with the name 3.0 vs 4.1 but I can’t figure where I have to change 
> …)
> 
>  
> 
>  
> 
> Do anybody have an idea?
> 
>  
> 
> Regards,
> 
>  
> 
>  
> 
> M Olivier CLAUDE- PhD Student
> 
> INSERM/UPMC UMRS ICAN 1166 – Equipe 2
> 
> Faculté de médecine Pitié-Salpêtrière
> 
> 91, bld de l'Hôpital - 3ème étage - Porte 305
> 
> 75013 Paris
> 
>  
> 
>  
> 
> 
> 
> 
> ___
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> 
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Re: [galaxy-dev] Tmhmm and signal P

[Olivier CLAUDE]

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 such file or 
directory)
Signal: ERROR in sequence file(s), check syntax

In galaxy report :

Fatal error : exit code 127 ()
/bin/sh: 1 : signal: not found
One or more tasks failed, e.g. 127 from 'signalp -short -t euk 
 
mailto:bjoern.gruen...@gmail.com] 
Envoyé : jeudi 12 novembre 2015 12:48
À : Olivier CLAUDE 
Cc : 'galaxy-dev' 
Objet : Re: [galaxy-dev] Tmhmm and signal P

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

> 
> With v4.1 it can’t be reached by galaxy (I am thinking 
> about something with the name 3.0 vs 4.1 but I can’t figure where I 
> have to change …)
> 
>  
> 
>  
> 
> Do anybody have an idea?
> 
>  
> 
> Regards,
> 
>  
> 
>  
> 
> M Olivier CLAUDE- PhD Student
> 
> INSERM/UPMC UMRS ICAN 1166 – Equipe 2
> 
> Faculté de médecine Pitié-Salpêtrière
> 
> 91, bld de l'Hôpital - 3ème étage - Porte 305
> 
> 75013 Paris
> 
>  
> 
>  
> 
> 
> 
> 
> ___
> 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:
>   https://lists.galaxyproject.org/
> 
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>   http://galaxyproject.org/search/mailinglists/
> 
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Re: [galaxy-dev] Tmhmm and signal P

[Peter Cock]

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 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 such file or 
> directory)
> Signal: ERROR in sequence file(s), check syntax

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:

$ signalp -G -t euk does_not_exist.faa
gawk: /mnt/galaxy/opt/signalp-3.0/bin/in2how+fasta:84: fatal: cannot
open file `does_not_exist.faa' for reading (No such file or directory)
signalp: ERROR in sequence file(s), check syntax

Which folder were you in, and did the test/test.seq file exist relative to it?

But in any case, good news that signalp appears to be on your $PATH

> In galaxy report :
>
> Fatal error : exit code 127 ()
> /bin/sh: 1 : signal: not found
> One or more tasks failed, e.g. 127 from 'signalp -short -t euk 
>  
> 

I'm guessing there is another copy-and-paste error here, with
"signal" rather than "signalp". Perhaps your email editor is
being too helpful with auto-correction?

When you ran signalp at the command line by hand, were you
doing it as the Galaxy Linux user, or with your personal account?
They probably have different $PATH settings.

>
> That's all.
> Thank you for your help again .
>
> Olivier.

Thanks Bjoern :)

Peter
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Re: [galaxy-dev] Tmhmm and signal P

[Olivier CLAUDE]

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:
>$ signalp -G -t euk does_not_exist.faa
>gawk: /mnt/galaxy/opt/signalp-3.0/bin/in2how+fasta:84: fatal: cannot open file 
>`does_not_exist.faa' for reading (No such file or directory)
>signalp: ERROR in sequence file(s), check syntax

For the "$SIGNALP" I just wrote what was written in the readme file,
If I open the "signalp" file, I can see on line 17 "SIGNALP=/signal-3.0"
I assume that when I writ $SIGNALP it refers to this path?
My email editor changed "signalp" in"Signalp" and in"signal" in my previous 
message :'(

>Which folder were you in, and did the test/test.seq file exist relative to it?

I was in "~/signal-3.0" and the file "/test/test.seq" exists. I kept the 
structure from the archive, I did not wanted to change everything.


>But in any case, good news that signalp appears to be on your $PATH 

I had to write in in the .bashrc of my account otherwise I had to export it 
everytime.

>I'm guessing there is another copy-and-paste error here, with "signal" rather 
>than "signalp". Perhaps your email editor is being too helpful with 
>auto-correction?

I just checked and yes it seems that he is too helpful.

>When you ran signalp at the command line by hand, were you doing it as the 
>Galaxy Linux user, or with your personal account?
>They probably have different $PATH settings.

I have only one account one this machine. Is  Galaxy considered as another user?
I installed it as a simple user, to avoid all the problems with the rights with 
the root.

Thanks again,

Olivier



-Message d'origine-
De : Peter Cock [mailto:p.j.a.c...@googlemail.com] 
Envoyé : jeudi 12 novembre 2015 14:22
À : Olivier CLAUDE 
Cc : Björn Grüning ; galaxy-dev 

Objet : Re: [galaxy-dev] Tmhmm and signal P

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 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 such 
> file or directory)
> Signal: ERROR in sequence file(s), check syntax

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:

$ signalp -G -t euk does_not_exist.faa
gawk: /mnt/galaxy/opt/signalp-3.0/bin/in2how+fasta:84: fatal: cannot open file 
`does_not_exist.faa' for reading (No such file or directory)
signalp: ERROR in sequence file(s), check syntax

Which folder were you in, and did the test/test.seq file exist relative to it?

But in any case, good news that signalp appears to be on your $PATH

> In galaxy report :
>
> Fatal error : exit code 127 ()
> /bin/sh: 1 : signal: not found
> One or more tasks failed, e.g. 127 from 'signalp -short -t euk 
>  
> 

I'm guessing there is another copy-and-paste error here, with "signal" rather 
than "signalp". Perhaps your email editor is being too helpful with 
auto-correction?

When you ran signalp at the command line by hand, were you doing it as the 
Galaxy Linux user, or with your personal account?
They probably have different $PATH settings.

>
> That's all.
> Thank you for your help again .
>
> Olivier.

Thanks Bjoern :)

Peter
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Re: [galaxy-dev] ProFTPD with SQLite

[Mic]

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 access to INSTALLATION.log.
If I press repair repository button then NGINX complain with an error 400.
Therefore, I also started to try to convert you Dockerfiles to a VM image.

How do you handle broken tools and how do you repair them in a Docker
container. I really like your Dockerfiles.

Thank you in advance.

Mic


On Thu, Nov 12, 2015 at 9:42 PM, Björn Grüning 
wrote:

> 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:
> >
> > *sudo aptitude install ProFTPD proftpd-mod-sqlite sqlite3*
> >
> > Unfortunately, I do not know how to connect the ProFTPD with Galaxy's
> > SQLite.
>
> ProFTP is an FTP Server and SQLite is a database you cannot connect from
> the one the the other.
>
> Are you still using the Galaxy Docker? If so we have already installed a
> FTP Server for you and configured it so Galaxy can talk to the FTP server.
>
> Please see the documentation about the Docker FTP server:
> https://github.com/bgruening/docker-galaxy-stable
>
> To transfer data from your client to Galaxy you only need an FTP cient.
> Have a look at Filezilla as FTP-client.
>
> Cheers,
> Bjoern
>
> > Thank you in advance.
> >
> > Mic
> >
> >
> >
> > ___
> > 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:
> >   https://lists.galaxyproject.org/
> >
> > To search Galaxy mailing lists use the unified search at:
> >   http://galaxyproject.org/search/mailinglists/
> >
>
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[galaxy-dev] Tool request: Integration von SecretomeP v1.0 in Galaxy

[Florian Sigloch]

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 SecretomeP v2.0 is available at
http://www.cbs.dtu.dk/services/SecretomeP/
However, it is restricted to 100 uploaded sequences, so processing of
large datasets is tedious. Therefore, integration into Galaxy would be
great!

A portable version of SecretomeP exists and is available here:
http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?secretomep
It is only v1.0, but the difference between the versions is minimal (see
also attached email of the developers).

There is one caveat: SecretomeP can deal with sequences only up to 4,000
amino acids (I am not sure, if including or excluding the 4,000). It
would be great to integrate a small preselection to sort out longer
sequences into the Galaxy tool.

Kind regards,
Florian Sigloch

P.S.: I am currently writing up my PhD thesis and I am short on time.
Would it be possible to integrate SecretomeP in 2-4 weeks? Please?
P.P.S.: I have been in contact with Dr. Björn Grüning about this, but I
do not want to bother him during his current trip to the US.
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Re: [galaxy-dev] Tmhmm and signal P

[Peter Cock]

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 tmhmm-2.0c.Linux.tar.gz which can
be uncompressed in the usual way

$ tar -zxvf tmhmm-2.0c.Linux.tar.gz

We also move this to /usr/opt/timhmm-2.0c for consistency with
SIGNALP, and create the link in /usr/local/bin:

$ sudo cp -R tmhmm-2.0c/ /usr/opt
$ sudo ln -s /usr/opt/tmhmm-2.0c/bin/tmhmm /usr/local/bin/

We needed to modify the main TMHMM script and tmhmmformat.pl to point
it at the right Perl on the system, replace the first line:

#!/usr/local/bin/perl

with:

#!/usr/bin/env perl

Also at about line 17, set the path to match what you've used:

$opt_basedir = '/usr/opt/tmhmm-2.0c';

You can change the defaults in this script too, but the Galaxy wrapper
should not mind.

Peter
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