Re: If you need students for small bioinformatics projects

[merlettaia]

Hi Afif,

There is no need to apologize - It's ok.
I've told Bioinformatics Institute mentors about Debian Med Team and told
you about them. I think it would be good if you'll write them - to ensure
they'll mail you when they'll search for mentors next time, and it might
happen that you'll have enough time and they'll have student who will be
glad to work on your project.
Thank you for your project idea link, I'll forward your letter to them if
you don't mind - to let them know that you might be interested next term
(or next year - or at least somewhen :)).

BTW, I was not precise in my previous letter - they are non-profit
organization and they don't charge any fees from students or mentors -
except time consumption :)

2016-09-11 0:26 GMT+03:00 Afif Elghraoui :

>
>
> على السبت 10 أيلول 2016 ‫14:23، كتب Afif Elghraoui:
> > It is a very nice idea and I
> > hope we could take advantage of it.
>
> Too many vague pronouns-- The program looks like a very nice idea and I
> hope that Debian Med could take advantage of it sometime.
>
> apologies for the ambiguity
>
Afif
>
> --
> Afif Elghraoui | عفيف الغراوي
> http://afif.ghraoui.name
>
>


-- 
Best wishes,
Tanya.

Re: Packaging BLAT for Debian

[Andreas Tille]

Hi again,

I'd like to pick up the ball for blat again.  For me it is not yet clear
by what license blat is covered and what might be the role of the KentLib
library[1] plays.  Is it possible to link blat against KentLib and is it
sensible to start packaging this first.

Just to let you know:  The freeze for the next Debian release is coming
soon and it blat should be distributed with the next release we should
hurry up to get this done.  For me it remains unclear who is responsible
for what and role the different pieces of code are playing.

Kind regards

  Andreas.

[1] https://github.com/jstjohn/KentLib

On Thu, Feb 27, 2014 at 12:49:06AM -0800, Jim Kent wrote:
> Yes.  If you could reiterate some of the links,  or if you prefer just
> forward this whole thread to Hiram, it would be great.   Then I can go back
> to wrestling with the ENCODE monster!
> 
> 
> On Thu, Feb 27, 2014 at 12:31 AM, Andreas Tille  wrote:
> 
> > Hi Jim,
> >
> > seems like we got in contact to the perfectly right time. :-)
> >
> > I'm happily waiting for your colleagues showing up at the Debian Med
> > list (which I'd strongly recommend for this purpose since I'm just a
> > member of the team and not the whole team ;-)) and repeat that one of
> > them might be interested in our Mentoring of the Month effort
> >
> >https://wiki.debian.org/DebianMed/MoM
> >
> > Looking forward to a great cooperation
> >
> > Andreas.
> >
> > On Thu, Feb 27, 2014 at 12:17:09AM -0800, Jim Kent wrote:
> > > Disabling the pslCheck seems like the sensible and pragmatic thing.
> > >
> > > I'm going to write a short note introducing you to Hiram Clawson, and
> > also
> > > Ann Zweig our project manager (and Hiram's boss).  It is actually part of
> > > our grant to package the tools in ways to make it easier for people to
> > use
> > > them.   Our current system is not so bad, but it requires people to
> > > actually read the README, and set an environment variable.   This was
> > state
> > > of the art in 1985, but not the
> > > config
> > > make
> > > make install
> > > people are used to these days,  never mind a RPM or anything more recent,
> > >  and most of the younger programmers get lost.
> > >
> > > I do think we want to do some renaming of directories and the like as
> > part
> > > of this process, and ideally end up with all the code that is under one
> > > license under the same subdirectory.  It's somewhat close to that, but
> > > there are enough exceptions to be a pain.   We switched from CVS to git
> > > about 2 years ago in large part to make moving directories around much
> > less
> > > of a pain in the butt, so we _can_ do this now,  but it's been sort of a
> > > back burner thing, and is only about 10% complete.
> > >
> > > Anyway,  we are paid by the taxpayers to do this sort of work, and will
> > > make some time for it.   We would welcome your help,  and getting it into
> > > Debian is as good a starting point as any,  better than most if we have
> > > support from that group.
> > >
> > > Take care,
> > >  Jim
> > >
> > >
> > >
> > > On Wed, Feb 26, 2014 at 11:16 PM, Andreas Tille 
> > wrote:
> > >
> > > > Hi Jim,
> > > >
> > > > On Wed, Feb 26, 2014 at 10:33:59PM -0800, Jim Kent wrote:
> > > > > I'm glad you isolated it to the -O2.
> > > >
> > > > :-)
> > > >
> > > > > I don't think there's a super easy way to cut pslCheck out of the
> > whole
> > > > > 1,200,000 UCSC genomics source tree.
> > > >
> > > > For the moment I simply disabled this check.  I guess it is also this
> > > > way sufficient to detect potential problems (and it was not the
> > pslCheck
> > > > that failed in the first place).
> > > >
> > > > > I would, on the other hand, be very
> > > > > happy for you to take on the job of packaging up that whole source
> > tree
> > > > for
> > > > > Debian.   I could refer you to a less busy member of my staff,  Hiram
> > > > > Clawson,  who has a _lot_ of experience helping people get that to
> > build.
> > > >
> > > > This is a very cool offer.  I actually have thought about packaging the
> > > > whole UCSC genomics source tree as well since it obviously contains
> > > > several tools that perfectly fit in our scope.  I wonder whether Hiram
> > > > might even like to learn something about Debian packaging.  In our team
> > > > we have quite some tradition in mentoring people as you can see here:
> > > >
> > > >https://wiki.debian.org/DebianMed/MoM
> > > >
> > > > Perhaps it comes handy if somebody in your team is capable to create
> > > > Debian packages which in the end is not more than wrapping up the build
> > > > process into some sceme.
> > > >
> > > > BTW, when I inspected the jksrc source tree (and also in the specific
> > > > case of the blat source) I realised that it might make real sense to
> > > > enable dynamic linking of the tools against the static libraries you
> > are
> > > > creating.  The Debian way to do this would be to create two 

Re: If you need students for small bioinformatics projects

[Afif Elghraoui]

على السبت 10 أيلول 2016 ‫14:23، كتب Afif Elghraoui:
> It is a very nice idea and I
> hope we could take advantage of it.

Too many vague pronouns-- The program looks like a very nice idea and I
hope that Debian Med could take advantage of it sometime.

apologies for the ambiguity
Afif

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

Re: If you need students for small bioinformatics projects

[Afif Elghraoui]

Hi, Tanya,

Many thanks for taking the time to write this message. I do have at
least one idea [1] that might fit well for this, but I wouldn't be able
to participate--at least for this cycle. It is a very nice idea and I
hope we could take advantage of it.

Thanks and regards
Afif

1. https://lists.debian.org/debian-med/2016/07/msg00088.html

على السبت  3 أيلول 2016 ‫17:03، كتب merlettaia:
> Hi All,
> 
> I’m writing you in case if someone has a small research
> bioinformatics-related project to this academic term and wishes to find
> some smart student (or students) to do it.
> 
> Our St.Petersburg’s local bioinformatics school (named Bioinformatics
> Institute) provides 1-year study program in bioinformatics for
> biologists and software developers (this year ~40 students applied). It
> is additional education program, and combines lectures every Saturday
> (except holidays) with 1 course project for fall and spring terms +
> summer internship.
> 
> For now they are looking mentors, who could provide projects and guide
> students to do them.
> 
> Project supervising  can be done remotely, for example, via Skype or
> email. It would be good if you could provide 1 hour per week. For
> student study project should take approximately 10 hours per week. This
> semester they start learning bioinformatics, and probably couldn’t do
> too complex tasks (of course, it depends on student personality).
> 
> 
> I should also mention that at my university (named “Academic
> University”) this 1-year course is included to Master degree education
> program. It means that some of this year’s students are studying at this
> program now.
> 
> Since this is a part of main education for them, this course project
> means *a lot*. They'll be expelled if they do nothing useful. And that's
> why they will do their best not too fail (there is also a very tough
> selection to this MSc program and a very saturated program in fall
> semester in 1st year of education - so please don't push too hard! 2nd
> MSc program students are also interested in course projects - since in
> fall they are usually starting to write their thesis and look for thesis
> mentor - you may provide project for them also).
> 
> Other students should be also good and most probably could communicate
> in English (but you can interview them to be sure).
> 
> Here are basic projects requirements:
> 
>   *
> 
> for 1 student, or for a team (1 student with biological + 1 with
> software development or CS background)
> 
>   *
> 
> project can be done for 3 months
> 
>   *
> 
> not very difficult project where you can guide
> 
>   *
> 
> educational :)
> 
> I believe there is no fee for mentoring, scholarship for students is
> fully optional (in most cases there is no scholarships). But I may be
> wrong, because I haven’t tried mentoring before - for sure it is never
> mentioned in registration forms for mentors or elsewhere :)
> 
> Projects will be announced at September, 17th. Mentors wish to see them
> by September, 10th.
> 
> If you are interested, you can write to team (at)
> bioinformaticsinstitute.ru  to ask
> for details and describe your project. They have a Google Doc for
> project descriptions, but for now it is available only in Russian, I
> think if you’ll just write them and describe your project it will be ok
> (or I can give you a link to it).
> 
> 
> I could also help you while mentoring since I live in St.Petersburg and
> can go at that school at Saturday to find your student and try to
> persuade him/her not to be lazy :) Or even I can help them with some
> basic knowledge and/or coding - if you’ll decide to provide something
> related to structural bioinformatics, I’ll be happy to be involved =)
> 
> 
> -- 
> Regards,
> Tanya.
> 
> P.S. - I've also told this school's mentors about Outreachy internships
> program, but not sure if they'll decide to mention it. Some of my
> friends know about it and they are interested in bioinformatics-related
> projects. Andreas, I hope you are reading and will use this knowledge
> for a great good :)
> P.-P. S. - I just thought that it might help some of you to accelerate
> your work or research. That's why I finally decided to write this.

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

Bug#837355: RM: vxl -- ROM; RC buggy, alternative available

[Andreas Tille]

Package: ftp.debian.org
Severity: normal

As discussed on Debian Med mailing list[1] this package is not as
recent as the code maintained inside ITK.  Since it is RC buggy it
would be better to remove it.

Kind regards

Andreas.


[1] https://lists.debian.org/debian-med/2016/09/msg00042.html

Re: Again help needed to upgrade picard-tools

[Andreas Tille]

On Sat, Sep 10, 2016 at 07:35:36PM +0100, Sascha Steinbiss wrote:
> 
> OK, great. The override is gone now and javahelper’s default mechanism works 
> perfectly.

Confirmed and uploaded.

Kind regards

 Andreas.

-- 
http://fam-tille.de

Re: Again help needed to upgrade picard-tools

[Sascha Steinbiss]

Hi,

>> ... 
>> Results: FAILURE (1833 tests, 1832 successes, 1 failures, 0 skipped)
>> ...
>> Any ideas from someone with more detailed insight?
> 
> We needed to exclude some tests since internet access is needed.  I have
> not checked the lot of output but this might be the case here as well
> (if a debuild on your local machine that's most probably the case).  So
> excluding another test would be no big deal.

It seemed to have been related to the method creating the test data not 
matching the method consuming it. Fixed it and tests complete now, also did 
some housekeeping. If you want to take a look, it’s in git. Should be ready for 
upload IMHO.

I was a bit confused by the ‘-gradle’ version suffix used in the previous 
version that was compensated for in an jh_installlibs override. If this suffix 
is not part of a new version string, jar renaming is broken during the 
installation. I removed the jh_installlibs override to make the current version 
work, but not being a core Java guy I was wondering whether this was a commonly 
used thing…?

Cheers
Sascha

Re: Again help needed to upgrade picard-tools

[Sascha Steinbiss]

Hi all,

> seems I always have trouble with picard-tools.  I have injected new
> upstream version in Git but it fails to build.  The upgrade of
> libhtsjdk-java went fine but it would be great if somebody could have a
> look at picard-tools.

Something in the build system changed; I patched it slightly to work again.
Builds now with libhtsjdk-java 2.6, but one test fails at the moment:

Gradle Test Executor 1 finished executing tests.
Results: FAILURE (1833 tests, 1832 successes, 1 failures, 0 skipped)

Here’s the output from the test’s HTML report:

org.testng.internal.reflect.MethodMatcherException: 
Data provider mismatch
Method: runCollectTargetedMetricsTest([Parameter{index=0, 
type=java.lang.String, declaredAnnotations=[]}, Parameter{index=1, 
type=java.lang.String, declaredAnnotations=[]}, Parameter{index=2, 
type=java.lang.String, declaredAnnotations=[]}, Parameter{index=3, 
type=java.lang.String, declaredAnnotations=[]}, Parameter{index=4, type=int, 
declaredAnnotations=[]}, Parameter{index=5, type=int, declaredAnnotations=[]}, 
Parameter{index=6, type=boolean, declaredAnnotations=[]}, Parameter{index=7, 
type=int, declaredAnnotations=[]}, Parameter{index=8, type=int, 
declaredAnnotations=[]}, Parameter{index=9, type=double, 
declaredAnnotations=[]}, Parameter{index=10, type=double, 
declaredAnnotations=[]}, Parameter{index=11, type=double, 
declaredAnnotations=[]}, Parameter{index=12, type=double, 
declaredAnnotations=[]}, Parameter{index=13, type=int, declaredAnnotations=[]}])
Arguments: 
[(java.lang.String)testdata/picard/analysis/directed/CollectHsMetrics/lowmapq.sam,(java.lang.String)testdata/picard/analysis/directed/CollectHsMetrics/chrM.fasta,(java.lang.String)testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list,(java.lang.String)NONE,(java.lang.Integer)2,(java.lang.Integer)0,(java.lang.Boolean)true,(java.lang.Integer)2,(java.lang.Integer)202,(java.lang.Integer)0,(java.lang.Double)0.0,(java.lang.Double)0.505,(java.lang.Double)0.0,(java.lang.Integer)1000]
at 
org.testng.internal.reflect.DataProviderMethodMatcher.getConformingArguments(DataProviderMethodMatcher.java:52)
at org.testng.internal.Invoker.injectParameters(Invoker.java:1225)
at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1123)
at 
org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129)
at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
at org.testng.TestRunner.privateRun(TestRunner.java:746)
at org.testng.TestRunner.run(TestRunner.java:600)
at org.testng.SuiteRunner.runTest(SuiteRunner.java:366)
at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:361)
at org.testng.SuiteRunner.privateRun(SuiteRunner.java:319)
at org.testng.SuiteRunner.run(SuiteRunner.java:268)
at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
at org.testng.TestNG.runSuitesSequentially(TestNG.java:1264)
at org.testng.TestNG.runSuitesLocally(TestNG.java:1189)
at org.testng.TestNG.runSuites(TestNG.java:1104)
at org.testng.TestNG.run(TestNG.java:1076)
at 
org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:133)
at 
org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:83)
at 
org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:61)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at 
org.gradle.messaging.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35)
at 
org.gradle.messaging.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
at 
org.gradle.messaging.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:32)
at 
org.gradle.messaging.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:93)
at com.sun.proxy.$Proxy2.stop(Unknown Source)
at 
org.gradle.api.internal.tasks.testing.worker.TestWorker.stop(TestWorker.java:120)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at 
org.gradle.messaging.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:35)
at 

Re: Again help needed to upgrade picard-tools

[Andreas Tille]

Hi Sascha,

On Sat, Sep 10, 2016 at 03:11:32PM +0100, Sascha Steinbiss wrote:
> 
> Something in the build system changed; I patched it slightly to work again.
> Builds now with libhtsjdk-java 2.6, but one test fails at the moment:

Good!

> ... 
> Results: FAILURE (1833 tests, 1832 successes, 1 failures, 0 skipped)
>  ...
> Any ideas from someone with more detailed insight?

We needed to exclude some tests since internet access is needed.  I have
not checked the lot of output but this might be the case here as well
(if a debuild on your local machine that's most probably the case).  So
excluding another test would be no big deal.

Thanks for checking

 Andreas.

-- 
http://fam-tille.de

Again help needed to upgrade picard-tools

[Andreas Tille]

Hi,

seems I always have trouble with picard-tools.  I have injected new
upstream version in Git but it fails to build.  The upgrade of
libhtsjdk-java went fine but it would be great if somebody could have a
look at picard-tools.

Thanks a lot

   Andreas.

-- 
http://fam-tille.de