On Mon, Oct 21, 2013 at 12:11 PM, Eric Rasche rasche.eric@yandex.ru wrote:
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
Hello all,
At my organisation's instance of galaxy, we have some connectors to talk to chado (inserting/removing GenBank & GFF files, etc).
That sounds awesome! Is that open source or are there plans to make this available?
However, for one of the workflows we plan to use, there is a script which must be run which has no input files and no output files (gmod_add_organism.pl, for those curious). This script *must* be run before another script is run (gmod_bulk_load_gff3.pl), or the database insert will fail
So my question is: Is there an easy way to specify dependencies when they depend on external factors, rather than just input/output files?
As far as I am aware there is no such mechanism in place. I would create a Trello issue if you feel this should be added - it is certainly not an unreasonable request. My sense however is the Galaxy concept of a tool and workflow are very coupled to file inputs and outputs at this time, so I am not certain we will be able to get to this request quickly.
For now, my recommendation would be just to use a dummy input and output file. You can even create a file type that is only used for this purpose to limit confusion. Can you find some logging statements or something to populate this file with?
Hope this helps and let us know if there are any additional questions, -John
If there isn't a generalised mechanism to do this, should I just list input and output files that are never actually created or removed?
Cheers, Eric
Eric Rasche Programmer II Center for Phage Technology Texas A&M University College Station, TX 77843 404-692-2048 esr@tamu.edu rasche.eric@yandex.ru -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/
iQIcBAEBAgAGBQJSZWA0AAoJEMqDXdrsMcpVGBUP/izaBVdCMR8ezm+5GNDpbsiZ CohkkFFZluewd14a08Mmgv42atmqAD10YiJAr1p5xu2eDB5OQJSH7dqXEbAS3IaL IhmfCkZdyd/+FUbOHwcS1AQ/XGWCQlahoME3sPsNOJM0Ru1jwA/Z4w7+CwZ0VSmy ooqExkS87S3wLzzflivqBnu40de1vWt33mIIbPRUDukPHQRPZMDNRPtAhUE2mL52 nkuUfhgcSNjyIYnCEqCNq5xd+sACepLB5F3LtszdmMgd9jjAJVcXqeXugiN4TSeI arMlzmPq2uIhDNKqx/ljsA9GqgrsLI+WJ2EvbTirAAvbcPVZDUCEMuRc7tMluSfp J8wU4wu2h2J3KvTIbOYiP0eudTTzDdfBvkNV4Zdvygv9WdNutFbLvwiNMt7FiUVI gq3/Mq95J74UahL9NeuG02vpMCRChigMG6cXjCaZfAlnubjbdLZ56XF/XVQeRaoz MnW35R7Y3ER46eFzSq6hU1Xlsjq2I5Esm4yx2O5Rs7Ieu4MSHdz7SV6qkGX32dVC ajSfue/zPd4DEj83mFrZjcjpax7YNF006CrWyBftC5dPKWfftuqy1Uhl2EZuscPI I8dliTrT0DIHJX5GqhqoMuX4iq5rN1WhSVB0N+HQZDt1nhHyiWyO/7zb0n6sHPv/ E9D2qOO7jYL++b6oTIT9 =RQ0Y -----END PGP SIGNATURE----- ___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/