Re: Adding Rostlab packages to our tasks files
Thank you for the suggestions, I am going to implement them right now.
I did not know that I was could maintain these tasks (bio and bio-dev). Now that you drew my attention to it, I am going to add all our packages.
* Is there a list of and a description for the fields that can appear in the tasks files like 'Published-Title', 'Remark', 'X-Remark' asf? - can
you please point me to it?
* Is there a way to give multiple citations for one package, like in the yaml file of disulfinder? Could the citations not be automatically
extracted from the upstream-metadata.yaml file for this page?
Ah, I see I can /not/ commit to the tasks (svn: Can't create directory '/svn/blends/db/transactions/3112-1.txn': Permission denied), so I attach
the diff (tasks.diff). The most important is to add 'profphd' to the tasks as well.
* So seeing that I can not change the task files, how should I do it?: ask you or Steffen to change it for me?
* I am now going to update the links on our wiki page.
Thank you for helping us with the proper maintenance of these tasks!
On 10/01/12 08:59, Andreas Tille wrote:
> by chance I had a look into the packages in trunk/packages/rostlab/.
> When doing so I noticed that not all of these are mentioned in our tasks
> file. This is important to enable easy installation via metapackages
> as well as advertising our pages in the web sentinel at
> BTW, I stumbled upon the WIki page from Rostlab at
> and it seems that not every information about the Debian packaged
> software is up to date. If I where you I would probably try to link to
> the according packages.debian.org page or alternatively to the
> corresponding entry in the web sentinel above (just append #pkgname to
> the link above) which is probably even more helpfull to guide the user
> to relevant packages with one click.
> I would like you to review ma decisions to insert the missing packages
> below into bio and bio-dev task. Is this OK for you?
> Kind regards
> ----- Forwarded message from firstname.lastname@example.org -----
> Date: Tue, 10 Jan 2012 07:43:03 -0000
> From: email@example.com
> To: firstname.lastname@example.org
> Subject: r3111 - in /projects/med/trunk/debian-med/tasks:
> bio bio-dev
> Author: tille
> Date: Tue Jan 10 07:43:02 2012
> New Revision: 3111
> URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3111
> Added Rostlab packages to according tasks
> Modified: projects/med/trunk/debian-med/tasks/bio
> URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=3111&op=diff
> --- projects/med/trunk/debian-med/tasks/bio (original)
> +++ projects/med/trunk/debian-med/tasks/bio Tue Jan 10 07:43:02 2012
> @@ -3005,9 +3005,11 @@
> Depends: abacas
> -Depends: profnet-bval, profnet-chop, profnet-con, profnet-isis, profnet-md, profnet-norsnet, profnet-prof, profnet-snapfun, profphd-net
> +Depends: profnet-bval, profnet-chop, profnet-con, profnet-isis, profnet-md, profnet-norsnet, profnet-prof, profnet-snapfun
> X-Remark: The profnet homepage contains an image of a complete Debian system. The Debian Med
> team tries to support the authors by providing binary packages inside Debian.
> +Depends: profphd-net, profphd-utils
> Depends: abyss
> Published-Title: ABySS: A parallel assembler for short read sequence data
> @@ -3029,6 +3031,8 @@
> Depends: populations
> Depends: raccoon
> +Depends: librg-utils-perl
> Depends: snap
> Published-Authors: I. Korf
> @@ -3854,6 +3858,9 @@
> University of California, Berkeley Departments of Mathematics and
> Molecular and Cell Biology.
> +Depends: reprof
> +Responsible: Peter Hoenigschmid <email@example.com>
> +Homepage: https://www.rostlab.org/owiki/index.php/Packages
> Comment: Several related R packages are listed at CRAN:
> Modified: projects/med/trunk/debian-med/tasks/bio-dev
> URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio-dev?rev=3111&op=diff
> --- projects/med/trunk/debian-med/tasks/bio-dev (original)
> +++ projects/med/trunk/debian-med/tasks/bio-dev Tue Jan 10 07:43:02 2012
> @@ -68,6 +68,8 @@
> Depends: libstaden-read-dev
> Depends: libsrf-dev
> +Depends: libzerg-dev, libzerg-perl
> Suggests: r-cran-rocr
> Why: Even if this package is not directly connected to biology it is maintained by
> Blends-commit mailing list
> ----- End forwarded message -----
--- bio-dev (revision 3112)
+++ bio-dev (working copy)
@@ -70,6 +70,12 @@
Depends: libzerg-dev, libzerg-perl
+Published-Title: Zerg: a very fast BLAST parser library.
+Published-Authors: Paquola, ApuÃ£ C M, Machado, Abimael A, Reis, Eduardo M, Da Silva, Aline M, and Verjovski-Almeida, Sergio
+Published-In: Bioinformatics. 19(8):1035-6
Why: Even if this package is not directly connected to biology it is maintained by
--- bio (revision 3112)
+++ bio (working copy)
@@ -3011,6 +3011,14 @@
Depends: profphd-net, profphd-utils
+Published-Title: Combining evolutionary information and neural networks to predict protein secondary structure.
+Published-Authors: Rost, B. and Sander, C.
+Published-In: Proteins. 19(1):55-72
Published-Title: ABySS: A parallel assembler for short read sequence data
Published-Authors: Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I
@@ -3025,6 +3033,12 @@
+Published-Title: DISULFIND: a disulfide bonding state and cysteine connectivity prediction server.
+Published-Authors: A. Ceroni and A. Passerini and A. Vullo and P. Frasconi
+Published-In: Nucleic Acids Res. 34:W177-81
@@ -3869,7 +3883,7 @@
'reprof' is an improved implementation of 'prof', a popular protein secondary
structure and accessibility predictor. Prediction is either
done from protein sequence alone or from an alignment - the latter should be
- used for optimal performance.
+ used for optimal performance.
This package provides the 'reprof' command. It is only a command line
interface to the functionality provided by the modules in