From: Ghiban, C. <gh...@cs...> - 2009-12-09 20:24:27
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Hi Scott, I'm fine with File::Temp as long as the path is writable. Thanks, Cornel -----Original Message----- From: Scott Cain [mailto:sc...@sc...] Sent: Wednesday, December 09, 2009 3:22 PM To: Ghiban, Cornel Cc: GMOD Schema/Chado List; gmod-devel Subject: Re: [Gmod-schema] Upcoming release of chado/gmod-1.1 Cornel, About alternate tmp directories: would you rather be able to specify yourself what directory to use, or tell the loader to use a random tmp directory a la File::Temp? Using File::Temp would make life easier, since it would deal with cleanup afterwards. Scott On Wed, Dec 9, 2009 at 3:06 PM, Scott Cain <sc...@sc...> wrote: > Hi Cornel, > > Thanks for the suggestions; see my comments below. > > Scott > > On Wed, Dec 9, 2009 at 2:51 PM, Ghiban, Cornel <gh...@cs...> wrote: >> Hi Scott, >> >> I have two ideas for gmod_bulk_load_gff3.pl >> >> 1. Could you please add a switch "-silent" or "-quiet", that would >> inhibit all the warnings and the debug messages > > There are currently debugging messages that only print out if $DEBUG > is set, so you actually are only seeing "normal" messages (and yes, > there are quite a few of them). Adding a quiet flag might take a > little extra work, and I'll assign it a fairly low priority, > especially since you can achieve the same result by executing the > command and adding ">/dev/null" to the command. > >> 2. At some point there are some temporary files created. Would it be possible for these file to be created in /tmp or add a switch so the user may set this path. Currently I can't launch gmod_bulk_load_gff3.pl from a web environment unless I make some edits. >> > > I thought I'd already implemented this, but looking at the bulk > loader, I see that I didn't. I probably had a conversation with you > and said something like "that should be easy to do" and later in my > head the got converted to "that was easy to do" :-) I'll work on that > today. > > Scott > > >> Thanks, >> Cornel >> >> -----Original Message----- >> From: Scott Cain [mailto:sc...@sc...] >> Sent: Wednesday, December 09, 2009 2:40 PM >> To: GMOD Schema/Chado List; gmod-devel >> Subject: [Gmod-schema] Upcoming release of chado/gmod-1.1 >> >> Hi all, >> >> I am preparing for the 1.1 release of gmod/chado and would like to know if there is anything on anybody's wish list for fixes or (minor) additions before the release. We've made lots of improvements and fixes over the past year, so you may want to take a look at the Changes file to see what has been done: >> >> >> http://gmod.svn.sourceforge.net/viewvc/gmod/schema/trunk/chado/Change >> s >> >> I will be checking with the bug and feature request trackers over the >> next few days in case you post there instead of replying to this >> email: >> >> https://sourceforge.net/tracker/?group_id=27707&atid=391294 >> https://sourceforge.net/tracker/?group_id=27707&atid=391291 >> >> Thanks, >> Scott >> >> -- >> --------------------------------------------------------------------- >> --- Scott Cain, Ph. D. scott at >> scottcain dot net GMOD Coordinator (http://gmod.org/) >> 216-392-3087 Ontario Institute for Cancer Research >> >> --------------------------------------------------------------------- >> --------- >> Return on Information: >> Google Enterprise Search pays you back Get the facts. >> http://p.sf.net/sfu/google-dev2dev >> _______________________________________________ >> Gmod-schema mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-schema >> > > > > -- > ---------------------------------------------------------------------- > -- Scott Cain, Ph. D. scott at > scottcain dot net GMOD Coordinator (http://gmod.org/) > 216-392-3087 Ontario Institute for Cancer Research > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |