Re: [GSoC] ncbi-blast+ and htslib uploaded
Moved tigr-glimmer to Git. I'll answer more detailed tomorrow since I
was offline today. Kind regards, Andreas.
On Thu, Aug 11, 2016 at 09:29:10AM +0300, Canberk Koç wrote:
> Hello Andreas,
>
> I make a suit for tigr-glimmer but package in SVN can you please move it to
> git.
>
> Best Regards
>
>
>
> Canberk Koç
> [image: https://]about.me/canberkkoc
> <https://about.me/canberkkoc?promo=email_sig&utm_source=email_sig&utm_medium=email_sig&utm_campaign=external_links>
>
> 2016-08-11 8:10 GMT+03:00 Canberk Koç <canberkkoc@gmail.com>:
>
> > Hello Andreas,
> >
> > I commit Cd-Hit according to it's manual but these example codes did not
> > work also there is no command like cd-hit when i install the program. So as
> > you say i commit it with errors in test so we can figure it our together .
> >
> > Best Regards
> >
> >
> >
> > Canberk Koç
> > [image: https://]about.me/canberkkoc
> >
> > <https://about.me/canberkkoc?promo=email_sig&utm_source=email_sig&utm_medium=email_sig&utm_campaign=external_links>
> >
> > 2016-08-09 10:59 GMT+03:00 Canberk Koç <canberkkoc@gmail.com>:
> >
> >> Hello Andreas,
> >>
> >> I'll gladly do tests and keep going before end of the year i think we can
> >> manage to cover most of packages. Tools6 issue i'll make partial test to
> >> blast2 and binaries packages in it if i stuck i'll inform you again i am
> >> going on. Thanks for help.
> >>
> >> Best Regards
> >>
> >>
> >>
> >> Canberk Koç
> >> [image: https://]about.me/canberkkoc
> >>
> >> <https://about.me/canberkkoc?promo=email_sig&utm_source=email_sig&utm_medium=email_sig&utm_campaign=external_links>
> >>
> >> 2016-08-09 9:38 GMT+03:00 Andreas Tille <andreas@fam-tille.de>:
> >>
> >>> Hi Canberk,
> >>>
> >>> On Tue, Aug 09, 2016 at 07:46:26AM +0300, Canberk Koç wrote:
> >>> > I make a little test for Emboss.
> >>> > I found there is a test directory in this package but tests are not
> >>> > complete i think ,
> >>> > make check did not do anything useful so they will add tests to the
> >>> > package i assume .
> >>>
> >>> OK, having at least some partial test is better than no test at all.
> >>>
> >>> Where the hints for ncbi-tools6 by Aaron and me helpful?
> >>>
> >>> > Another issue GSoC send me an email again and final evaluation is on 15
> >>> > august for students so i'll send them commits how is our progress you
> >>> think
> >>> > ?
> >>>
> >>> I admit I would have hoped that we would manage more packages at the end
> >>> but the second half went better than the first. It would be great if
> >>> you could keep on adding tests even after GSoC has finished and we might
> >>> manage to get tests for most of the Debian Med packages until Freeze for
> >>> Debian 9 (about end of the year).
> >>>
> >>> > I have a question also how can i find which packages i committed with a
> >>> > script what should i use ?
> >>>
> >>> You could query the public UDD mirror via
> >>>
> >>> PGPASSWORD="public-udd-mirror" psql --host=public-udd-mirror.xvm.m
> >>> it.edu --username=public-udd-mirror udd
> >>>
> >>> The following query is an example how to get those packages featuring
> >>> you as changelog owner and adding the Vcs URL in Git.
> >>>
> >>> udd=> SELECT DISTINCT u.source, u.version, s.vcs_url FROM upload_history
> >>> u JOIN sources s ON u.source = s.source WHERE changed_by_email = '
> >>> canberkkoc@gmail.com' and s.release='sid' and s.vcs_url not like 'svn%'
> >>> order by u.source ;
> >>> source | version |
> >>> vcs_url
> >>> -------------+-------------------+--------------------------
> >>> -----------------------------------------------
> >>> amap-align | 2.2-6 | https://anonscm.debian.org/git
> >>> /debian-med/amap-align.git
> >>> bwa | 0.7.15-2 | https://anonscm.debian.org/git
> >>> /debian-med/bwa.git
> >>> clustalo | 1.2.2-1 | https://anonscm.debian.org/git
> >>> /debian-med/clustalo.git
> >>> clustalw | 2.1+lgpl-5 | https://anonscm.debian.org/git
> >>> /debian-med/clustalw.git
> >>> dialign | 2.2.1-8 | https://anonscm.debian.org/git
> >>> /debian-med/dialign.git
> >>> exonerate | 2.4.0-2 | https://anonscm.debian.org/git
> >>> /debian-med/exonerate.git
> >>> fastqc | 0.11.5+dfsg-3 | https://anonscm.debian.org/git
> >>> /debian-med/fastqc.git
> >>> gdpc | 2.2.5-6 | https://anonscm.debian.org/git
> >>> /debian-med/gdpc.git
> >>> hmmer | 3.1b2+dfsg-1 | https://anonscm.debian.org/git
> >>> /debian-med/hmmer.git
> >>> hmmer2 | 2.3.2-10 | https://anonscm.debian.org/git
> >>> /debian-med/hmmer2.git
> >>> htslib | 1.3.1-2 | https://anonscm.debian.org/git
> >>> /debian-med/htslib.git
> >>> infernal | 1.1.1-5 | https://anonscm.debian.org/git
> >>> /debian-med/infernal.git
> >>> kalign | 1:2.03+20110620-3 | https://anonscm.debian.org/git
> >>> /debian-med/kalign.git
> >>> mummer | 3.23+dfsg-1 | https://anonscm.debian.org/git
> >>> /debian-med/mummer.git
> >>> muscle | 1:3.8.31+dfsg-2 | https://anonscm.debian.org/git
> >>> /debian-med/muscle.git
> >>> ncbi-blast+ | 2.3.0-2 | https://anonscm.debian.org/git
> >>> /debian-med/ncbi-blast+.git
> >>> phylip | 1:3.696+dfsg-3 | https://anonscm.debian.org/git
> >>> /debian-med/phylip.git
> >>> primer3 | 2.3.7-2 | https://anonscm.debian.org/git
> >>> /debian-med/primer3.git
> >>> probcons | 1.12-11 | https://anonscm.debian.org/git
> >>> /debian-med/probcons.git
> >>> t-coffee | 11.00.8cbe486-4 | https://anonscm.debian.org/git
> >>> /debian-med/t-coffee.git
> >>> vcftools | 0.1.14+dfsg-3 | https://anonscm.debian.org/git
> >>> /debian-med/vcftools.git
> >>> (21 Zeilen)
> >>>
> >>> > Thanks for your help and support.
> >>>
> >>> You are welcome.
> >>>
> >>> Updated todo list:
> >>>
> >>> ncbi-tools6
> >>> njplot (according to manual there is an option without X11,
> >>> -> https://anonscm.debian.org/git/debian-med/njplot.git
> >>> picard-tools
> >>> cd-hit
> >>> tigr-glimmer
> >>>
> >>> Kind regards
> >>>
> >>> Andreas.
> >>>
> >>> --
> >>> http://fam-tille.de
> >>>
> >>
> >>
> >
--
http://fam-tille.de
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