[Beg-bogas] start update routine (message to genome admins)
dear all, since today I improved the checkandstart update script of BOGAS/ORCAE from now on it's not needed anymore to manually add your genome in that script, he will check to list of genomes (once a day) from the bogas config file ! still one drawback, he is reading the file that is in my SVN ... but unfortunately I don't have a neat and easy solution for that currently :-/ ays, L. -- ============================================================== Lieven Sterck, PhD Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck@psb.vib-ugent.be Website: http://bioinformatics.psb.ugent.be ============================================================== "Facts are meaningless. You could use facts to prove anything that's even remotely true" - H. Simpson
Lieven, why don't you put/extract this kind of info from a table in the bogas_bogas database? This way people can add/remove genomes without being tight to 1 person's account/files. Stephane On 15/07/2012 23:23, Lieven Sterck wrote:
dear all,
since today I improved the checkandstart update script of BOGAS/ORCAE from now on it's not needed anymore to manually add your genome in that script, he will check to list of genomes (once a day) from the bogas config file! still one drawback, he is reading the file that is in my SVN ... but unfortunately I don't have a neat and easy solution for that currently :-/
ays, L.
-- ============================================================== Lieven Sterck, PhD
Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck@psb.vib-ugent.be Website: http://bioinformatics.psb.ugent.be
============================================================== "Facts are meaningless. You could use facts to prove anything that's even remotely true" - H. Simpson
_______________________________________________ Beg-bogas mailing list Beg-bogas@psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/beg-bogas
-- ================================================================== Stephane Rombauts Principal Scientific staff Bioinformatics & Systems Biology Division Tel:+32 (0)9 331 38 21 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM strom@psb.vib-ugent.be http://bioinformatics.psb.ugent.be/ ==================================================================
Dear all, yet another update on the update routine. to start off I added a new security level to be used in the conf.yaml files: hidden: has the same effect as 'develop' (= it's not shown on the public home page, not even in the restricted list, but it appears on on your personal homepage if you have access to it) but the main diff is that those genomes are being processed by the normal update routine in stead of the development version of it. now for the update routine itself: I modified all the scripts such that they read their config info from the BOGAS/ORCAE production version directory (in stead of my svn version) so now as soon as a new species has been added in the prod version it will be incorporated in the update routine automatically. there is however one tradeoff: the update routine is now using the BOGAS/ORCAE perl modules located in /group/biocomp/projects/BOGAS! (the permissions are group writeable, so it is possible to bugfix/extend them if needed) I just ask one favour in return that, although only putting your conf files in the prod dir will do the trick, you also update/add them in your svn so that we still have all recent stuff available in the svn. This is important when (hopefully soon) we definitely switch to ORCAE and that at that point I don't have to start gathering all versions and info from several locations! thanks and enjoy! L. ----- Original Message -----
From: "stephane Rombauts" <stephane.rombauts@psb.vib-ugent.be> To: beg-bogas@psb.vib-ugent.be Sent: Monday, 16 July, 2012 11:22:58 AM Subject: Re: [Beg-bogas] start update routine (message to genome admins)
Lieven,
why don't you put/extract this kind of info from a table in the bogas_bogas database? This way people can add/remove genomes without being tight to 1 person's account/files.
Stephane
On 15/07/2012 23:23, Lieven Sterck wrote:
dear all,
since today I improved the checkandstart update script of BOGAS/ORCAE
from now on it's not needed anymore to manually add your genome in that script, he will check to list of genomes (once a day) from the bogas config file!
still one drawback, he is reading the file that is in my SVN ... but unfortunately I don't have a neat and easy solution for that currently :-/
ays,
L.
--
==============================================================
Lieven Sterck, PhD
Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology, UGent
Bioinformatics and Evolutionary Genomics Division
Technologiepark 927, B-9052 Gent, Belgium
Email: lieven.sterck@psb.vib-ugent.be
Website: http://bioinformatics.psb.ugent.be
==============================================================
"Facts are meaningless. You could use facts to prove anything
that's even remotely true" - H. Simpson
_______________________________________________
Beg-bogas mailing list Beg-bogas@psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/beg-bogas
-- ================================================================== Stephane Rombauts Principal Scientific staff
Bioinformatics & Systems Biology Division Tel:+32 (0)9 331 38 21 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM strom@psb.vib-ugent.be http://bioinformatics.psb.ugent.be/ ================================================================== _______________________________________________ Beg-bogas mailing list Beg-bogas@psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/beg-bogas
-- ============================================================== Lieven Sterck, PhD Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck@psb.vib-ugent.be Website: http://bioinformatics.psb.ugent.be ============================================================== "Facts are meaningless. You could use facts to prove anything that's even remotely true" - H. Simpson
participants (2)
-
Lieven Sterck -
stephane Rombauts