date:20161021

Re: [galaxy-dev] Tool needs a particular file extension -- now Datatype help

2016-10-21 Thread Steve Cassidy

Thanks all,
  it seems that my real problem is that the audio file (.wav) is not being 
identified as a valid datatype and ending up as a zero length text file. So, I 
need to start to explore the world of datatypes.

Following the docs 
(https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes) I can 
modify datatypes_conf.xml in my Galaxy sources and add a new datatype for wav 
files:

http://web.science.mq.edu.au/~cassidy

On 21 Oct. 2016, at 12:58 pm, Peter Cock 
> wrote:

Using a soft link for this is a common pattern, and should be followed with &&
(ideally using XML CDATA to avoid escaping everything like  etc),
and quote the filenames just in case there are any spaces. e.g.

https://github.com/galaxyproject/tools-iuc/blob/master/tools/trinity/run_de_analysis.xml#L16


For reference, in tools-iuc there are over 400 soft link examples:

$ grep "ln -s" tools/*/*.xml | wc -l
446

Peter

On Fri, Oct 21, 2016 at 5:48 PM, Steve Cassidy  wrote:
Hi,
I’m wrapping a tool that needs it’s input to have a known file extension
(an audio file, eg. .wav).  Since Galaxy stores all data as .dat files the
tool is falling over since it doesn’t know what .dat is.

I thought I’d be able to get around this by hard linking the .dat file to
the same name with a .wav extension (dataset_1.dat.wav), this works when I
try it with the tool on the command line but within Galaxy it fails, here’s
my :

   ln $signal ${signal}.wav 
   /home/maus/maus OUTFORMAT=TextGrid LANGUAGE=$language
   BPF=$bpf INSKANTEXTGRID=$inskantextgrid
INSORTTEXTGRID=$insorttextgrid
   MODUS=$modus MAUSSHIFT=$mausshift MINPAUSLEN=$minpauslen
WEIGHT=$weight
   INSPROB=$insprob NOINITIALFINALSILENCE=$noinitialfinalsilence
OUTSYMBOL=$outsymbol
   OUT=$output SIGNAL=${signal}.wav

resulting in the job command line:

ln /tmp/tmp7AZvx7/files/000/dataset_2.dat
/tmp/tmp7AZvx7/files/000/dataset_2.dat.wav & /home/maus/maus
OUTFORMAT=TextGrid LANGUAGE=aus BPF=/tmp/tmp7AZvx7/files/000/dataset_1.dat
INSKANTEXTGRID=false INSORTTEXTGRID=false MODUS=standard MAUSSHIFT=10
MINPAUSLEN=5 WEIGHT=7.0 INSPROB=0.0 NOINITIALFINALSILENCE=no OUTSYMBOL=sampa
OUT=/tmp/tmp7AZvx7/files/000/dataset_3.dat
SIGNAL=/tmp/tmp7AZvx7/files/000/dataset_2.dat.wav

I’m getting an error message from the tool:

sox FAIL formats: can't open input file
`/tmp/tmp7AZvx7/files/000/dataset_2.dat.wav': WAVE: RIFF header not found

this suggests that the hard link didn’t get made.  I tried copying the file
instead but got the same result.

I could go in and patch the tool script to be more forgiving but it would be
good to find a solution that didn’t require that if possible.

Any pointers appreciated.

Steve
—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy


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[galaxy-dev] Local Galaxy Workflow Sharing

2016-10-21 Thread Rachel Bell

Hi,


I am looking to share a workflow I've created in Local Galaxy with an 
individual user via email address - where they will access the workflow on main 
galaxy.

When I select 'Share/Download' the following error message appears:


[cid:59dde9c4-0f20-4cb6-9c14-1875f09657c4]


I'd really appreciate some guidance on this, I'm guessing it is maybe a 
permissions thing in one of the config files?


Thanks in advance,


Rachel Bell

Bioinformatics Technician

Premaitha Health

Rutherford House

Manchester Science Park

Manchester, M15 6SZ, UK

T: +44 (0) 161 667 1068

M: +44 (0) 7875 191 219

www.premaitha.com


This e-mail including any attachments is intended for the addressee only.  It 
is private and confidential.  If you have received this message in error, we 
apologise, but please notify us and remove it from your system. You must take 
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Premaitha Limited, trading as Premaitha Health, is registered in England with 
registered number 8436676. Its registered office is at Rutherford House, 
Manchester Science Park, Manchester, M15 6SZ, UK.
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Re: [galaxy-dev] Tool needs a particular file extension

2016-10-21 Thread Peter Cock

Using a soft link for this is a common pattern, and should be followed with &&
(ideally using XML CDATA to avoid escaping everything like  etc),
and quote the filenames just in case there are any spaces. e.g.

https://github.com/galaxyproject/tools-iuc/blob/master/tools/trinity/run_de_analysis.xml#L16


For reference, in tools-iuc there are over 400 soft link examples:

$ grep "ln -s" tools/*/*.xml | wc -l
 446

Peter

On Fri, Oct 21, 2016 at 5:48 PM, Steve Cassidy  wrote:
> Hi,
>  I’m wrapping a tool that needs it’s input to have a known file extension
> (an audio file, eg. .wav).  Since Galaxy stores all data as .dat files the
> tool is falling over since it doesn’t know what .dat is.
>
> I thought I’d be able to get around this by hard linking the .dat file to
> the same name with a .wav extension (dataset_1.dat.wav), this works when I
> try it with the tool on the command line but within Galaxy it fails, here’s
> my :
>
> ln $signal ${signal}.wav 
> /home/maus/maus OUTFORMAT=TextGrid LANGUAGE=$language
> BPF=$bpf INSKANTEXTGRID=$inskantextgrid
> INSORTTEXTGRID=$insorttextgrid
> MODUS=$modus MAUSSHIFT=$mausshift MINPAUSLEN=$minpauslen
> WEIGHT=$weight
> INSPROB=$insprob NOINITIALFINALSILENCE=$noinitialfinalsilence
> OUTSYMBOL=$outsymbol
> OUT=$output SIGNAL=${signal}.wav
>
> resulting in the job command line:
>
> ln /tmp/tmp7AZvx7/files/000/dataset_2.dat
> /tmp/tmp7AZvx7/files/000/dataset_2.dat.wav & /home/maus/maus
> OUTFORMAT=TextGrid LANGUAGE=aus BPF=/tmp/tmp7AZvx7/files/000/dataset_1.dat
> INSKANTEXTGRID=false INSORTTEXTGRID=false MODUS=standard MAUSSHIFT=10
> MINPAUSLEN=5 WEIGHT=7.0 INSPROB=0.0 NOINITIALFINALSILENCE=no OUTSYMBOL=sampa
> OUT=/tmp/tmp7AZvx7/files/000/dataset_3.dat
> SIGNAL=/tmp/tmp7AZvx7/files/000/dataset_2.dat.wav
>
> I’m getting an error message from the tool:
>
> sox FAIL formats: can't open input file
> `/tmp/tmp7AZvx7/files/000/dataset_2.dat.wav': WAVE: RIFF header not found
>
> this suggests that the hard link didn’t get made.  I tried copying the file
> instead but got the same result.
>
> I could go in and patch the tool script to be more forgiving but it would be
> good to find a solution that didn’t require that if possible.
>
> Any pointers appreciated.
>
> Steve
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
>
>
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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>
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Re: [galaxy-dev] Tool needs a particular file extension

2016-10-21 Thread Léo Biscassi

Hi Steve, try do like this example [1]

[1]
https://github.com/leobiscassi/autodock_vina_tools/blob/dev/tools/prepare_ligand/prepare_ligand.xml

Cheers,

On Fri, Oct 21, 2016 at 2:48 PM Steve Cassidy 
wrote:

> Hi,
>  I’m wrapping a tool that needs it’s input to have a known file extension
> (an audio file, eg. .wav).  Since Galaxy stores all data as .dat files the
> tool is falling over since it doesn’t know what .dat is.
>
> I thought I’d be able to get around this by hard linking the .dat file to
> the same name with a .wav extension (dataset_1.dat.wav), this works when I
> try it with the tool on the command line but within Galaxy it fails, here’s
> my :
>
> ln $signal* ${signal}.wav* 
> /home/maus/maus OUTFORMAT=TextGrid LANGUAGE=$language
> BPF=$bpf INSKANTEXTGRID=$inskantextgrid
> INSORTTEXTGRID=$insorttextgrid
> MODUS=$modus MAUSSHIFT=$mausshift MINPAUSLEN=$minpauslen
> WEIGHT=$weight
> INSPROB=$insprob NOINITIALFINALSILENCE=$noinitialfinalsilence
> OUTSYMBOL=$outsymbol
> OUT=$output *SIGNAL=${signal}.wav*
>
> resulting in the job command line:
>
> ln /tmp/tmp7AZvx7/files/000/dataset_2.dat
> */tmp/tmp7AZvx7/files/000/dataset_2.dat.wav* &
> /home/maus/maus OUTFORMAT=TextGrid LANGUAGE=aus
> BPF=/tmp/tmp7AZvx7/files/000/dataset_1.dat
> INSKANTEXTGRID=false INSORTTEXTGRID=false MODUS=standard MAUSSHIFT=10
> MINPAUSLEN=5 WEIGHT=7.0 INSPROB=0.0
> NOINITIALFINALSILENCE=no OUTSYMBOL=sampa
> OUT=/tmp/tmp7AZvx7/files/000/dataset_3.dat SIGNAL=
> */tmp/tmp7AZvx7/files/000/dataset_2.dat.wav*
>
> I’m getting an error message from the tool:
>
>
> *sox FAIL formats: can't open input file
> `/tmp/tmp7AZvx7/files/000/dataset_2.dat.wav': WAVE: RIFF header not found *
> this suggests that the hard link didn’t get made.  I tried copying the
> file instead but got the same result.
>
> I could go in and patch the tool script to be more forgiving but it would
> be good to find a solution that didn’t require that if possible.
>
> Any pointers appreciated.
>
> Steve
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
>
> ___
> 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/

-- 
Best regards,
*Léo Biscassi*
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[galaxy-dev] Tool needs a particular file extension

2016-10-21 Thread Steve Cassidy

Hi,
 I’m wrapping a tool that needs it’s input to have a known file extension (an 
audio file, eg. .wav).  Since Galaxy stores all data as .dat files the tool is 
falling over since it doesn’t know what .dat is.

I thought I’d be able to get around this by hard linking the .dat file to the 
same name with a .wav extension (dataset_1.dat.wav), this works when I try it 
with the tool on the command line but within Galaxy it fails, here’s my 
:

ln $signal ${signal}.wav 
/home/maus/maus OUTFORMAT=TextGrid LANGUAGE=$language
BPF=$bpf INSKANTEXTGRID=$inskantextgrid INSORTTEXTGRID=$insorttextgrid
MODUS=$modus MAUSSHIFT=$mausshift MINPAUSLEN=$minpauslen WEIGHT=$weight
INSPROB=$insprob NOINITIALFINALSILENCE=$noinitialfinalsilence 
OUTSYMBOL=$outsymbol
OUT=$output SIGNAL=${signal}.wav

resulting in the job command line:

ln /tmp/tmp7AZvx7/files/000/dataset_2.dat 
/tmp/tmp7AZvx7/files/000/dataset_2.dat.wav & /home/maus/maus OUTFORMAT=TextGrid 
LANGUAGE=aus BPF=/tmp/tmp7AZvx7/files/000/dataset_1.dat INSKANTEXTGRID=false 
INSORTTEXTGRID=false MODUS=standard MAUSSHIFT=10 MINPAUSLEN=5 WEIGHT=7.0 
INSPROB=0.0 NOINITIALFINALSILENCE=no OUTSYMBOL=sampa 
OUT=/tmp/tmp7AZvx7/files/000/dataset_3.dat 
SIGNAL=/tmp/tmp7AZvx7/files/000/dataset_2.dat.wav

I’m getting an error message from the tool:

sox FAIL formats: can't open input file 
`/tmp/tmp7AZvx7/files/000/dataset_2.dat.wav': WAVE: RIFF header not found

this suggests that the hard link didn’t get made.  I tried copying the file 
instead but got the same result.

I could go in and patch the tool script to be more forgiving but it would be 
good to find a solution that didn’t require that if possible.

Any pointers appreciated.

Steve
—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] Changing Tool Shed URL

2016-10-21 Thread Martin Čech

Thank you very much for sharing Youssef. Very helpful.

Martin

On Fri, Oct 21, 2016 at 10:20 AM Youssef GHORBAL 
wrote:

> Hello,
>
> Two other tables need to be adapated (they reference tool_id)
> Table “job" and table “workflow_step”
>
> Youssef Ghorbal
> Institut Pasteur
> -
> > On 21 Oct 2016, at 00:36, Youssef Ghorbal 
> wrote:
> >
> > Hello,
> >
> >   What worked for us was this action sequence :
> >   - stop Galaxy
> >   - update config/tool_sheds_file.xml (change the URL from the old
> one to the new one)
> >   - “sed” shed_tool_conf.xml to change the “guid", the tool_shed and
> the “file” to replace the old prefix with the new prefix.
> >   - update the tool_version table (the tool_id column) to change the
> old prefix to the new prefix.
> >   - update the tool_shed_repositoriy table to change the tool_shed
> column to use the new tooshed prefix
> >   - update the directory shed_tools to rename the directory from the
> old prefix to the new prefix (care to adapt the subdirectories too :
> ./mytoolshed.url/xxx => ./mytoolshed2.url/)
> >   - start Galaxy (and cross your fingers)
> >
> >   Hope this help !
> >
> > Youssef Ghorbal
> > Institut Pasteur
> > -
> >> On 20 Oct 2016, at 00:16, Youssef GHORBAL 
> wrote:
> >>
> >> Hello,
> >>
> >>  I’m wondering if there is any way to change an established Tool
> Shed URL.
> >>  I have a Galaxy instance and a Tool Shed instance (
> http://mytoolshed.url/xxx) A lot of tools have beed installed from that
> Tool Shed inside Galaxy (tools referenced inside workflows etc)
> >>  I want to change the Tool Shed URL from http://mytoolshed.url/xxx
> to http://mytoolshed2.url/.
> >>
> >>  Galaxy and Tool Shed seems to use parts of the URL as a guid for
> tools.
> >>
> >>  Tool Shed does not seem to bother to be called by either URLs (it
> generates guids with the new URLs scheam for new tools though)
> >>
> >>  Galaxy does not seem to handle it, I changed the
> tool_sheds_conf.xml to point to new URL, but when I update a tool on the
> Tool Shed, Galaxy gets the new version but it generates buggy tool panel
> (the tool is cited twice)
> >>  I also tried to mess around with the shed_tool_conf.xml apdapting
> the guids and the  items with no luck.
> >>
> >>  Can someone point me to the right direction ? How the matching is
> done between shed_tool_conf.xml entries, the tool_version and
> tool_shed_repository tables.
> >>
> >>  Thank you for your help.
> >>
> >> Youssef Ghorbal
> >> Institut Pasteur
> >> ___
> >> 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/
> >
>
> ___
> 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:
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Re: [galaxy-dev] Changing Tool Shed URL

2016-10-21 Thread Youssef GHORBAL

Hello,

Two other tables need to be adapated (they reference tool_id)
Table “job" and table “workflow_step”

Youssef Ghorbal
Institut Pasteur
-
> On 21 Oct 2016, at 00:36, Youssef Ghorbal  wrote:
> 
> Hello,
>   
>   What worked for us was this action sequence :
>   - stop Galaxy
>   - update config/tool_sheds_file.xml (change the URL from the old one to 
> the new one)
>   - “sed” shed_tool_conf.xml to change the “guid", the tool_shed and the 
> “file” to replace the old prefix with the new prefix.
>   - update the tool_version table (the tool_id column) to change the old 
> prefix to the new prefix.
>   - update the tool_shed_repositoriy table to change the tool_shed column 
> to use the new tooshed prefix
>   - update the directory shed_tools to rename the directory from the old 
> prefix to the new prefix (care to adapt the subdirectories too : 
> ./mytoolshed.url/xxx => ./mytoolshed2.url/) 
>   - start Galaxy (and cross your fingers)
> 
>   Hope this help !
> 
> Youssef Ghorbal
> Institut Pasteur
> -
>> On 20 Oct 2016, at 00:16, Youssef GHORBAL  wrote:
>> 
>> Hello,
>> 
>>  I’m wondering if there is any way to change an established Tool Shed 
>> URL.
>>  I have a Galaxy instance and a Tool Shed instance 
>> (http://mytoolshed.url/xxx) A lot of tools have beed installed from that 
>> Tool Shed inside Galaxy (tools referenced inside workflows etc)
>>  I want to change the Tool Shed URL from http://mytoolshed.url/xxx to 
>> http://mytoolshed2.url/. 
>> 
>>  Galaxy and Tool Shed seems to use parts of the URL as a guid for tools.
>>  
>>  Tool Shed does not seem to bother to be called by either URLs (it 
>> generates guids with the new URLs scheam for new tools though)
>> 
>>  Galaxy does not seem to handle it, I changed the tool_sheds_conf.xml to 
>> point to new URL, but when I update a tool on the Tool Shed, Galaxy gets the 
>> new version but it generates buggy tool panel (the tool is cited twice)
>>  I also tried to mess around with the shed_tool_conf.xml apdapting the 
>> guids and the  items with no luck.
>> 
>>  Can someone point me to the right direction ? How the matching is done 
>> between shed_tool_conf.xml entries, the tool_version and 
>> tool_shed_repository tables.
>> 
>>  Thank you for your help.
>> 
>> Youssef Ghorbal
>> Institut Pasteur
>> ___
>> 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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Re: [galaxy-dev] Tool needs a particular file extension -- now Datatype help

[galaxy-dev] Local Galaxy Workflow Sharing

Re: [galaxy-dev] Tool needs a particular file extension

Re: [galaxy-dev] Tool needs a particular file extension

[galaxy-dev] Tool needs a particular file extension

Re: [galaxy-dev] Changing Tool Shed URL

Re: [galaxy-dev] Changing Tool Shed URL

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