Re: [galaxy-dev] simple example of composite data types
On Mon, May 18, 2015 at 1:55 PM, Brian Haas bh...@broadinstitute.org wrote: Thanks, Peter! I've verified that I can get your code to work - bundling the composite files. I'll keep plugging away at my little example and see if I can figure out what's going awry. more later. Thx again! Good luck - compound datatypes are one of the complex ways to extend Galaxy. If your code was online in GitHub or BitBucket, it would be easier for us (including the Galaxy team) to comment on. Regards, 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/
Re: [galaxy-dev] simple example of composite data types
I've uploaded my simple example here: https://github.com/brianjohnhaas/galaxy_composite_datatype_test I can't seem to get it to bundle the output files no matter what I've tried. Help is much appreciated. :) best, ~brian ___ 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/
Re: [galaxy-dev] simple example of composite data types
Thanks, Peter! I've verified that I can get your code to work - bundling the composite files. I'll keep plugging away at my little example and see if I can figure out what's going awry. more later. Thx again! ~brian ___ 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/
[galaxy-dev] alternative solution to logout ldap users
Hi,
I have configured apache as reverse proxy for galaxy and I also configured
apache to access my openldap for authentication. It's working fine but I
was getting some trouble to logout the users as explained in the
documentation here
https://wiki.galaxyproject.org/Admin/Config/ExternalUserAuth#Logging_out_Basic_Auth.27d_Users
So I tried a different approach by adding this mod_rewrite lines to my
apache vhost and it seems to work fine to logout users
RewriteEngine on
RewriteRule ^/user/logout$ https://logout@%{HTTP_HOST}; [R,L]
It took me some time to figure out this workaround so I send it to the list
in case it's useful for anyone else. It would be nice if someone can update
the docs. I have verified it works with latest chrome and firefox. It
doesn't work with internet explorer 11
regards
Pablo.
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Re: [galaxy-dev] simple example of composite data types
Hi Brian, Your original email with attachments has made it to the list now, http://dev.list.galaxyproject.org/difficulty-creating-composite-data-type-tp4667193.html Title: difficulty creating composite data type Peter On Mon, May 18, 2015 at 2:25 PM, Brian Haas bh...@broadinstitute.org wrote: In the next couple of hours, if I'm not able to resolve this, I'll post my ultra-simple example on github and I'll be grateful for others to take a look. cheers, ~brian ___ 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/
Re: [galaxy-dev] simple example of composite data types
Fantastic! I've actually made a few changes. I'm putting my latest code up on github now and will share it in just a moment. It'll be much easier this way - as you suggested. best, ~brian On Mon, May 18, 2015 at 9:58 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Brian, Your original email with attachments has made it to the list now, http://dev.list.galaxyproject.org/difficulty-creating-composite-data-type-tp4667193.html Title: difficulty creating composite data type Peter On Mon, May 18, 2015 at 2:25 PM, Brian Haas bh...@broadinstitute.org wrote: In the next couple of hours, if I'm not able to resolve this, I'll post my ultra-simple example on github and I'll be grateful for others to take a look. cheers, ~brian -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas ___ 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/
Re: [galaxy-dev] simple example of composite data types
Hi Peter, I'm actually more confused now that I was when I started... I was able to get your code working, focusing on the 'makeblastdb' with a nucleotide fasta file. I figured that experimenting with this example would lead to some key insights, particularly by dropping certain files that are stored as extra-files area. I copied everything over as a new tool, made it a new data type, and trimmed the blast.py code down to the bare essentials for testing just the nucleotide makeblastdb functionality. However, commenting out 'self.add_composite_file()' for various files had no effect - the files were still being stored. I then make 'composite_type = None' and it still stored the files to my dismay. Since I couldn't get my copy to work as I had expected, I went back over to your 'blast.py' and just commented out the ''self.add_composite_file()' lines and set 'composite_type = None' and no effect. Of course, I restarted galaxy after each modification, and could verify that it was reading the new files and had byte-compiled the py mods. I'm clearly not grasping something fundamental here. I can't get my code to bundle files, and I can't get your code to *not* bundle files. ;) Any ideas on where to go to troubleshoot this further? many thanks, ~brian ___ 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/
[galaxy-dev] Can a tool retrieve a user's API KEY?
I'm trying to create a tool that user's can use that will interact with Galaxy 's API, however the tool needs to be able to determine the user's API key.Is this possible? Can a tool determine what the user's API key is when the user actually runs the tool? ___ 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/
Re: [galaxy-dev] ldap module not present
I always recommend installing a virtualenv for Galaxy - and it should be pretty easy to install ldap into that with pip. But you are certainly right - longer term it probably makes sense to create a dynamic egg for this (for consistency if no other reason). I have created a Trello issue for that here - https://trello.com/c/szu6IZdh. Please vote. -John On Fri, May 15, 2015 at 12:10 PM, Will Holtz who...@lygos.com wrote: I'm trying out the new LDAP auth features in v15.05. I'm getting the following error in my logs: galaxy.auth.providers.ldap_ad DEBUG 2015-05-15 08:53:43,886 LDAP authenticate: could not load ldap module this is from 'import ldap' failing in lib/galaxy/auth/providers/ldap_ad.py Should there be some egg magic that takes care of this dependency for me? thanks, -Will -- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at who...@lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers). Please consider the environment before printing this email. ___ 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: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] simple example of composite data types
THANK YOU!!! :)
The fundamental piece that I was missing at:
https://wiki.galaxyproject.org/Admin/Datatypes/Composite%20Datatypes
was the
commandsomeTool.sh $input1 ${os.path.join( input1.extra_files_path,
'results.txt' )} ${os.path.join( input1.extra_files_path,
'results.dat' )} $output1/command
It would be great if the documentation could be updated a bit for clarity
on the importance of the '.extra_files_path', such as 'important: your tool
needs to create this directory and store the additional files that you want
there'.
This is a big leap forward for me. I'll now get on to testing the other
aspects of it. (still climbing the galaxy learning curve).
thanks again!
~brian
On Mon, May 18, 2015 at 2:39 PM, Daniel Blankenberg d...@bx.psu.edu wrote:
Hi Brian,
In your example tool, you need to pass “${ test_cdt.files_path } to your
perl script, which is a not-yet-existing directory for the files you want
to be part of the dataset’s extra files path.
Then you create that directory and place the files you want within that
directory.
Thanks for using Galaxy,
Dan
On May 18, 2015, at 2:02 PM, Brian Haas bh...@broadinstitute.org wrote:
Hi Peter,
I'm actually more confused now that I was when I started... I was able
to get your code working, focusing on the 'makeblastdb' with a nucleotide
fasta file. I figured that experimenting with this example would lead to
some key insights, particularly by dropping certain files that are stored
as extra-files area. I copied everything over as a new tool, made it a
new data type, and trimmed the blast.py code down to the bare essentials
for testing just the nucleotide makeblastdb functionality. However,
commenting out 'self.add_composite_file()' for various files had no effect
- the files were still being stored. I then make 'composite_type = None'
and it still stored the files to my dismay.
Since I couldn't get my copy to work as I had expected, I went back over
to your 'blast.py' and just commented out the ''self.add_composite_file()'
lines and set 'composite_type = None' and no effect.
Of course, I restarted galaxy after each modification, and could verify
that it was reading the new files and had byte-compiled the py mods.
I'm clearly not grasping something fundamental here. I can't get my
code to bundle files, and I can't get your code to *not* bundle files. ;)
Any ideas on where to go to troubleshoot this further?
many thanks,
~brian
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--
--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
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Re: [galaxy-dev] simple example of composite data types
I've updated my code, which now generates the .extra_files directory:
https://github.com/brianjohnhaas/galaxy_composite_datatype_test
I'm now trying to get the
composite_type = 'auto_primary_file*' *to work, but all I'm getting is an
empty file. My module code simply includes:
class CompositeDataTypeTest( Text ):
file_ext = 'cdt'
composite_type = 'auto_primary_file'
def generate_primary_file( self, dataset = None ):
log.debug(\n\n generate_primary_file() for Test data
###\n\n)
return('htmlbodymy test html/body/html')
and from what I can tell, the generate_primary_file() isn't being called,
as I'm not detecting the log entry in the console.
any ideas?
thanks in advance!
~brian
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Re: [galaxy-dev] simple example of composite data types
On Sun, May 17, 2015 at 5:44 PM, Brian Haas bh...@broadinstitute.org wrote: Greetings. Does anyone per chance have a simple working example of using composite data types? I've gotten as far as I can with the galaxy documentation, and I can't seem to get the additional files bundled into an extra files directory. (note, I have my example submitted w/ files attached, but currently pending moderator approval) much appreciated, ~brian Hi Brian, I can suggest looking at the BLAST database datatypes defined here: https://github.com/peterjc/galaxy_blast/tree/master/datatypes/blast_datatypes Also study the built in examples like HTML (with images as extra files): https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/data.py Regards, 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/
