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 <path/galaxy/database/tmp/tmpxxxx/signal.0.tmp > <path/galaxy/database/tmp/tmpxxxx/signal.0.tmp.out' gave: That's all. Thank you for your help again . Olivier. -----Message d'origine----- De : Björn Grüning [mailto:bjoern.gruening@gmail.com] Envoyé : jeudi 12 novembre 2015 12:48 À : Olivier CLAUDE <o.claude@outlook.fr> Cc : 'galaxy-dev' <galaxy-dev@lists.bx.psu.edu> 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/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

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=<path>/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.cock@googlemail.com] Envoyé : jeudi 12 novembre 2015 14:22 À : Olivier CLAUDE <o.claude@outlook.fr> Cc : Björn Grüning <bjoern.gruening@gmail.com>; galaxy-dev <galaxy-dev@lists.bx.psu.edu> Objet : Re: [galaxy-dev] Tmhmm and signal P Hi Olivier, On Thu, Nov 12, 2015 at 1:03 PM, Olivier CLAUDE <o.claude@outlook.fr> 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 <path/galaxy/database/tmp/tmpxxxx/signal.0.tmp > <path/galaxy/database/tmp/tmpxxxx/signal.0.tmp.out' gave:

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

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 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=<path>/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.cock@googlemail.com] Envoyé : jeudi 12 novembre 2015 14:22 À : Olivier CLAUDE <o.claude@outlook.fr> Cc : Björn Grüning <bjoern.gruening@gmail.com>; galaxy-dev <galaxy-dev@lists.bx.psu.edu> Objet : Re: [galaxy-dev] Tmhmm and signal P

Hi Olivier,

On Thu, Nov 12, 2015 at 1:03 PM, Olivier CLAUDE <o.claude@outlook.fr> 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 <path/galaxy/database/tmp/tmpxxxx/signal.0.tmp > <path/galaxy/database/tmp/tmpxxxx/signal.0.tmp.out' gave:

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

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 <path>/signal-3.0/tmp/TMP15....31945/plot.gnu"

I have restarted galaxy tried the same search, no changes in the output.

Any idea for tmhmm also?

-----Message d'origine----- De : Björn Grüning [mailto:bjoern.gruening@gmail.com] Envoyé : jeudi 12 novembre 2015 15:56 À : Olivier CLAUDE <o.claude@outlook.fr>; 'Peter Cock' <p.j.a.cock@googlemail.com> Cc : 'Björn Grüning' <bjoern.gruening@gmail.com>; 'galaxy-dev' <galaxy-dev@lists.bx.psu.edu> Objet : Re: [galaxy-dev] Tmhmm and signal P

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 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=<path>/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.cock@googlemail.com] Envoyé : jeudi 12 novembre 2015 14:22 À : Olivier CLAUDE <o.claude@outlook.fr> Cc : Björn Grüning <bjoern.gruening@gmail.com>; galaxy-dev <galaxy-dev@lists.bx.psu.edu> Objet : Re: [galaxy-dev] Tmhmm and signal P

Hi Olivier,

On Thu, Nov 12, 2015 at 1:03 PM, Olivier CLAUDE <o.claude@outlook.fr> 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 <path/galaxy/database/tmp/tmpxxxx/signal.0.tmp > <path/galaxy/database/tmp/tmpxxxx/signal.0.tmp.out' gave:

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

___________________________________________________________ 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/

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, rbrown1422@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 double-click it and then major issues. Attached is the problem button, and two other "Execute" buttons that work correctly -- one also involved in workflows. Thanks bob brown

___________________________________________________________ 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/

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.cock@googlemail.com] Envoyé : jeudi 12 novembre 2015 16:36 À : Björn Grüning <bjoern.gruening@gmail.com> Cc : Olivier CLAUDE <o.claude@outlook.fr>; galaxy-dev <galaxy-dev@lists.bx.psu.edu> Objet : Re: [galaxy-dev] Tmhmm and signal P On Thu, Nov 12, 2015 at 2:56 PM, Björn Grüning <bjoern.gruening@gmail.com> 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 can edit the SIGNALP=... line near the start of the signalp script - it defaults to /usr/opt/signalp-3.0/bin What we do is have a symbolic link (which is on the path) which points to the main script under /usr/opt/ or similar. These are my colleague's notes: <quote> SIGNALP arrives as the compressed file signalp-3.0.Linux.tar.Z, which can be uncompressed as usual: $ tar -zxvf signalp-3.0.Linux.tar.Z The resulting directory should be copied to /usr/opt/signalp-3.0 (this location is assumed by the SIGNALP scripts), and a symbolic link added to /usr/local/bin to enable command-line use. We also need to make the /usr/opt/signalp-3.0/tmp directory world-writable so that SIGNALP will run. $ sudo cp -R signalp-3.0/ /usr/opt/ $ sudo ln -s /usr/opt/signalp-3.0/signalp /usr/local/bin $ sudo chmod 777 /usr/opt/signalp-3.0/tmp </quote> If you don't have sudo rights, a little more work is needed. We currently use $HOME/opt/signalp-3.0/ and $HOME/bin/signalp as a symlink to /mnt/galaxy/opt/signalp-3.0/signalp but this requires you edit the script line to record the alternative path as the SIGNALP variable. Peter

Hello, This is working! For signlaP and promoter at least. I still got this weird error with tmhmm ("no output from tmhmm") and I can't figure what's wrong . I experienced some problems at the beginning with signal and promoter, because I forgot to remove the path I've made in the .bashrc . They were broken in the /usr/local/bin If anybody experience the problem in the future, just remove the old ones, remove from the path the wrong one, and redo the command line. Thanks a lot. Do anybody knows where i can find WolFPSORT? The website semms to be down for a while now and I am not able to find it anywhere? Thanks again! Olivier . -----Message d'origine----- De : Peter Cock [mailto:p.j.a.cock@googlemail.com] Envoyé : jeudi 12 novembre 2015 17:35 À : Olivier CLAUDE <o.claude@outlook.fr> Cc : Björn Grüning <bjoern.gruening@gmail.com>; galaxy-dev <galaxy-dev@lists.bx.psu.edu> Objet : Re: [galaxy-dev] Tmhmm and signal P On Thu, Nov 12, 2015 at 4:24 PM, Olivier CLAUDE <o.claude@outlook.fr> 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

Thnks for WolFPSORT, I have to check with my PI because we are uder the administrative supervision of 2 big public structures with very particular rules... About Tmhmm, it works. I've restarted galaxy, then the station and now everythings semms to be ok. Thank you for your time & help! Olivier On Fri, Nov 13, 2015 at 10:40 AM, Olivier CLAUDE <o.claude@outlook.fr> wrote:

Hello,

This is working! For signlaP and promoter at least.

Good.

I still got this weird error with tmhmm ("no output from tmhmm") and I can't figure what's wrong .

The message "no output from tmhmm" is from my wrapper script, https://github.com/peterjc/pico_galaxy/blob/master/tools/protein_analysis/tm... This can be triggered when tmhmm silently fails, e.g. you have just the 32bit binaries on a 64bit system: https://github.com/peterjc/pico_galaxy/commit/e79bc01a6e3ef68d21e0921cd65cd2... Can you run tmhmm successfully outside of Galaxy?

I experienced some problems at the beginning with signal and promoter, because I forgot to remove the path I've made in the .bashrc . They were broken in the /usr/local/bin If anybody experience the problem in the future, just remove the old ones, remove from the path the wrong one, and redo the command line.

Thanks a lot.

Do anybody knows where i can find WolFPSORT? The website semms to be down for a while now and I am not able to find it anywhere?

Thanks again!

Olivier .

Yes, http://wolfpsort.org/ is still down (and has been for some months so this is not a temporary glitch). The best plan would be to try to get in touch with Paul Horton. I will try to email him (and CC you). I do have a copy of WoLF PSORT v0.2 but this is not an open source tool, and redistribution is restricted. Assuming you want it for academic use only (so no commercial part-funding, no industry partnership, etc) than I can probably forward it to you off list. Peter -- WoLF PSORT Package Command Line Version 0.2 License Author: Paul Horton Copyright: All Rights Reserved Created: 2005/9/1 Last Modified: 2005/9/1 LICENSE 1. Academic License If you are an academic you may freely use this package on site or redistribute it for academic use as is. This does not include providing a WoLF PSORT prediction service over the internet. Academic citation would be highly appreciated. Non-profit use is a necessary condition for "academic". If in doubt please contact Paul Horton. 2. Commercial License Any rights not explicitly given in this license are reserved. However, any potential users are encouraged to contact Paul Horton to discuss other licensing arrangements.