On Mon, Oct 21, 2013 at 12:11 PM, Eric Rasche <rasche.e...@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 > e...@tamu.edu > rasche.e...@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/ ___________________________________________________________ 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/
