Re: Assistance with application task for "Quality assurance for biological and medical applications inside Debian"
Dear Shafeen, thanks a lot for your interest in Debian Med and our GSoC project. Since our main communication channel is the mailing list and I can not see anything private in your e-mail I take the freedom to CC my answer to the public list. (Hope this is OK for you.) On Mon, Mar 29, 2021 at 04:54:25AM +, Mohammed Rahman wrote: > Dear Mr. Andreas Tille, > > I hope you are doing well. My name is Shafeen Rahman and I’m currently > pursuing undergraduate studies at the University of Toronto in Canada. I am > reaching out to you in regards to the Debian Med related project you are in > charge of supervising for this year’s Google Summer of Code. > > I’ve enjoyed using Debian whether as a development environment, for my > personal computing usage, for server uses and my favourite experience, which > was using Debian to configure an open hardware microprocessor with my friends > to create an electric motor powered skateboard. From my positive experiences > with Debian, alongside reading the Debian Med team’s goal to enable > healthcare research with the power of free and open source software, I am > incredibly excited at the prospect of contributing to the Debian Project and > aiding the Debian Med team. Debian helped to drive an electric motor powered skateboard - how cool is this! ;-) > I bring intermediate university-level programming skills, having learned C > and shell scripting at a reliable level recently and having known other > languages like Java and Python for much longer. However, for any skills > missing I’ve seemed to excel where I’ve needed to grasp concepts and apply > them in time sensitive scenarios, such as in hackathons and a previous > internship experience. > > With that being said, I have attempted to follow through the recommended > reading and have been able to the point where I have a Debian unstable > environment working, with sbuild installed and seemingly ready to go. I’m > looking at attempting to fix bug #970312 (src:intake: Please provide > autopkgtest) which seems to ask the maintainer of the intake package to > provide a test suite for the package. From one of the examples listed, > snap-aligner, it seems that Mr. Pranav Ballaney creates a shell script that > compares the output of snap-aligner to the reference output. My first idea > seems to be to find the reference data for intake and write a shell script > for it, although I seem to be lost for next steps here. For this actual task it is not necessary but definitely helpful to have some background in bioinformatiks. Being a physicist myself I'm lacking this background as well and so its also not that straightforward to me to write test. Actual users of the programs are probably good in writing tests since they know how to use the program. In many cases reading the docs or even publications associated with the software in question might give helpful hints ... or just asking here on the mailing list can be a sensible way to learn how to write a sensible test command. But you can contribute in several ways to the Debian Med team in case you might realise that this kind of tasks is not feasible for you. > I’d greatly appreciate any pointers or tips on going about fixing this, or > next steps on the actual application for the Debian Med team (ie. is the > application process simply fixing a bug or are there also further steps?). There is no formal application for the Debian Med team. You definitely should subscribe our mailing list[1] and if you want to contribute code you should create a login on salsa[2] and ask for membership in med-team. > Thank you for your time, Hope this helps so far. Feel free to ask for more details. Kind regards Andreas. > Shafeen Rahman > (He/him) [1] https://lists.debian.org/debian-med [2] https://salsa.debian.org -- http://fam-tille.de
Re: Autopkgtest for Changeo
I have embedded the data and changed the autopkgtest. Kindly review. Thanking you, Regards Shruti ᐧ
Re: Outreachy project: complete workflows of tools
Hi, My name is Shruti. I have been contributing to Debian Med by writing autopkgtests for which I will be applying through GSoC this year. However, I came across this project which really interests me. I was initially planning on applying for this through Outreachy but unfortunately my application was not approved. I have a background in wet lab and I have worked extensively with RNA-Seq and microarray workflows for analysis of clinical data (particularly lymphoma). Last summer I worked on harmonising cell line datasets (RNA-Seq and microarray) to identify biomarkers and molecular signatures driving immune resistance for chemotherapy in DLBCL patients. I would be happy to learn other workflows such as microbiomes, CHiP-Seq etc if needed. I would love to be able to work on this project since it aligns with my skills sets, however I noticed that this project is not available through GSoC. Would it be possible to offer this project through GSoC as well so that I can submit a proposal for this? Thanking you, Regards Shruti On Mon, Mar 8, 2021 at 5:19 PM Tony Travis < tony.tra...@minke-informatics.co.uk> wrote: > On 07/03/2021 23:47, Tassia Camoes Araujo wrote: > > Hi all, > > > > On 2021-03-05 11:09, Tassia Camoes Araujo wrote: > >> [...] > >> Since deadline is approaching quickly, I suggest we move this off-list > >> and start writing in a wiki or pad. > > > > Here is my first draft, pasted below for your reference, but you can > > edit the text directly in this pad: > > > https://storm.debian.net/shared/OCYsOOEqJ5-CcfjVxIiye-ex-4LheegyP1pkIFghMKa > > > > Help needed to write the Intern tasks section. Also, please check if you > > have better scientific articles to recommend and list a few tools to be > > used in the starter tasks. > > > > Please help shaping this proposal so it ***really*** makes sense and > > attract interns ;-) > > Hi, Tassia. > > I recommend using "flexbar", which I use, instead of "Trimmomatic": > > > https://github.com/seqan/flexbar > > Also, depending on the sequencing technology used, consider assembling > short-paired-end reads with e.g. Pear: > > > https://github.com/tseemann/PEAR > > HTH, > >Tony. > > -- > Minke Informatics Limited, Registered in Scotland - Company No. SC419028 > Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) > tel. +44(0)19755 63548http://minke-informatics.co.uk > mob. +44(0)7985 078324mailto:tony.tra...@minke-informatics.co.uk > > ᐧ
Re: Autopkgtest for Changeo
Hi Shruti, On Mon, Mar 29, 2021 at 10:26:46PM +0530, Shruti Sridhar wrote: > I have embedded the data and changed the autopkgtest. > Kindly review. * Looks like you missed to commit the -data tarball to pristine-tar which the salsa CI job showed[1] - I fixed this one, CI looks better now. * Please note that the next revision for upload should have a higher version/revision than the one in the archive. Since current version is 1.0.2-1, your changelog ideally should have 1.0.2-2 as the changelog revision * The syntax for closing bug is "Closes: " your changes miss a colon there. * Since you are not in the uploaders field of this package, you need a "Team Upload" entry as the first changelog pointer Please take a look at my commits Other than these, your changes look good, however we are currently frozen[2] (i.e. we are in the process of making a new release) so none of these changes are appropriate for unstable at the moment. * Hence, next time (until we make a release) please create a d/experimental branch and commit stuff there - see kma package for example I will uploaded it to experimental for now, and will upload to unstable when new release is out. Thanks a lot for your work on this! :-) [1]: https://salsa.debian.org/med-team/changeo/-/jobs/1542592 [2]: https://release.debian.org/bullseye/freeze_policy.html Nilesh
