- beg-bogas@psb.ugent.be - maillist.psb.ugent.be

[Beg-bogas] [BOGAS] #180: change all DBI-containing scripts :D
by BOGAS 17 Nov '11

17 Nov '11

#180: change all DBI-containing scripts :D -------------------------+-------------------------------------------------- Reporter: brhel | Owner: liste Type: enhancement | Status: new Priority: major | Milestone: Component: Website | Version: Keywords: | -------------------------+-------------------------------------------------- at the moment, most BOGAS update / maintenance scripts are built like this: #============================== my @row = $sth->fetchrow_array; my $gene = $row[0]; my $structure = $row[2]; #============================== Problem: as soon as a new column is inserted in the table, the entire script fails, as the column order is important. That's why all my DBI-related scripts are built like this: #============================== my $row = $sth->fetchrow_hashref; my $structure = $row->{structure}; #============================== Independent of column order -> always correct even when the table undergoes major surgery :D So basically: change all scripts to be column order independent :) -- Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/180> BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas> Bioinformatics Online Genome Annotation Service

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[Beg-bogas] Out of Office: BOGAS - Eucalyptus grandis Annotation
by Kalluri, Udaya C. 10 Nov '11

10 Nov '11

I am currently out of office on maternity leave. Pllease contact Gail Hamilton (hamiltongr(a)ornl.gov<mailto:hamiltongr@ornl.gov>) for immediate assistance.

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Re: [Beg-bogas] BOGAS - Eucalyptus grandis Annotation
by Erich Bornberg 27 Oct '11

27 Oct '11

Thanks for your email. I am currently out of office but will try to catch up with emails from Oct. 30th onwards. EB

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[Beg-bogas] update error Connection
by liste＠psb.vib-ugent.be 27 Oct '11

27 Oct '11

2011/10/27 20:33:06 An error occured connecting to the database server Error message below: DBI connect('bogas_mipuc:psbsql04:3306','bogas',...) failed: Lost connection to MySQL server at 'reading authorization packet', system error: 0 at /www/group/biocomp/extra/bioinformatics_prod/webtools/sandbox/liste/BOGAS/trunk/src/perl/modules/BOGAS/DB.pm line 260

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[Beg-bogas] [BOGAS] #179: opsplitsen CACHE directory
by BOGAS 26 Oct '11

26 Oct '11

#179: opsplitsen CACHE directory -------------------------+-------------------------------------------------- Reporter: brhel | Owner: liste Type: enhancement | Status: new Priority: minor | Milestone: Component: Website | Version: Keywords: | -------------------------+-------------------------------------------------- momenteel wordt alles opgeslagen in één directory -> opsplitsen per genoom(versie) -- Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/179> BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas> Bioinformatics Online Genome Annotation Service

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[Beg-bogas] [BOGAS] #178: annotation summary table
by BOGAS 24 Oct '11

24 Oct '11

#178: annotation summary table -------------------------+-------------------------------------------------- Reporter: brhel | Owner: liste Type: enhancement | Status: new Priority: major | Milestone: Component: Website | Version: Keywords: | -------------------------+-------------------------------------------------- Het zu handig zijn om op de 'overview' pagina een tabel te hebben met de standaard annotatie statistieken: - aantal (multi-exon) genen - aantal introns - aantal EST-gevalideerde genen - aantal homology-supported genen - ... Natuurlijk zou deze tabel af en toe moeten geupdate worden -> via een cron-job elke week ofzo (indien er gewerkt is aan deze annotatie in die week; gemakkelijk te checken via de modification_date ) -- Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/178> BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas> Bioinformatics Online Genome Annotation Service

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[Beg-bogas] [BOGAS] #177: EST assignment -> UTR assignment problem
by BOGAS 24 Oct '11

24 Oct '11

#177: EST assignment -> UTR assignment problem ---------------------+------------------------------------------------------ Reporter: brhel | Owner: liste Type: defect | Status: new Priority: major | Milestone: Component: Website | Version: Keywords: | ---------------------+------------------------------------------------------ De volgende situatie doet zich voor: - een EST wordt toegekend aan een gen - de structuur van de EST komt niet overeen met het gen - de EST wordt wel gebruikt om de 'outer UTR' border van het gen te bepalen -> de EST staat nu op 'Y' ipv op 'N' -- Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/177> BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas> Bioinformatics Online Genome Annotation Service

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[Beg-bogas] Returned mail: see transcript for details
by Mail Delivery Subsystem 21 Oct '11

21 Oct '11

The original message was received at Fri, 21 Oct 2011 01:06:59 +0200 from localhost.localdomain [127.0.0.1] ----- The following addresses had permanent fatal errors ----- <dunan(a)lrsv.ups-tlse.fr> (reason: 550 5.1.1 <dunan(a)lrsv.ups-tlse.fr>: Recipient address rejected: User unknown in local recipient table) ----- Transcript of session follows ----- ... while talking to polext1.scsv.ups-tlse.fr.: >>> DATA <<< 550 5.1.1 <dunan(a)lrsv.ups-tlse.fr>: Recipient address rejected: User unknown in local recipient table 550 5.1.1 <dunan(a)lrsv.ups-tlse.fr>... User unknown <<< 554 5.5.1 Error: no valid recipients

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[Beg-bogas] [BOGAS] #176: change gene type
by BOGAS 17 Oct '11

17 Oct '11

#176: change gene type -------------------------+-------------------------------------------------- Reporter: brhel | Owner: Liste Type: enhancement | Status: new Priority: minor | Milestone: Component: Website | Version: Keywords: | -------------------------+-------------------------------------------------- It would be easy to allow rapid changes from 'mRNA' to 'pseudo' and vice versa. However, now I have to do these changes manually through psbsql04 -> For someone without access, it is not possible to do this! -- Ticket URL: <http://psbsvn01/trac/BOGAS/ticket/176> BOGAS <http://bioinformatics.psb.ugent.be/webtools/bogas> Bioinformatics Online Genome Annotation Service

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[Beg-bogas] Error in InterProScan job iprscan-20111014-0511426072174
by support＠ebi.ac.uk 14 Oct '11

14 Oct '11

System command [find] failed : cd /nfs/public/ro/es/appbin/linux-x86_64/iprscan-4.8/tmp/20111014/iprscan-20111014-0511426072174 && find /nfs/public/ro/es/appbin/linux-x86_64/iprscan-4.8/tmp/20111014/iprscan-20111014-0511426072174 -name \*.raw > /nfs/public/ro/es/appbin/linux-x86_64/iprscan-4.8/tmp/20111014/iprscan-20111014-0511426072174/merged.raw.files: exit status 1; No such file or directory -- 256 To help us solve the problem, please copy and paste this error and email it to the administrator <a href="mailto:support@ebi.ac.uk?subject=Error in InterProScan job iprscan-20111014-0511426072174">support(a)ebi.ac.uk</a>. Sorry about the inconvenience and thank you for using InterProScan.

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