Anton Kulaga

"bin/mango-submit -h" does not display anything

5

I am very confused by mango documentation When I do "bin/mango-submit -h" I do not get any output even though I have $SPARK_HOME setup in a right way.

SRR type now known

1

I am trying to download the following RNA-Seq dataset https://www.ncbi.nlm.nih.gov/sra/SRX313696[accn] with GEOParse However, it tell me that SRR filetype is not known

check for converted sra-s

1

If we are downloading with keep_sra=false and sra_format as fastq it makes sence to check for fast files and do not download sra-s if fastq files are avaliable and forcerewrite...

make case codecs from Seq[String]

1

There is very annoying 22 fields limitations for tuples in Scala that makes it problematic to work with csv-es with many headers. If for the codec I can provide Seq[String]...

It took me quite a lot to understand stopifnot(is(path, "character")) crashes caused by the following code: ``` base

Looks like https://pachterlab.github.io/sleuth_walkthroughs/trapnell/analysis.html is somewhat outdated, for instance ``` wget -O ../Trapnell_results.zip 'https://www.dropbox.com/s/eqx3jmylgns4wd3/Trapnell_results.zip?dl=1' ``` does not work

VEP problems

2

When I try to annotate the results with VEP I get: ``` WARNING: variant 259 on line 280 is too long to annotate: (78162751) WARNING: variant 260 on line 281...

ammonite does not import ammonite scripts with several @ properly

3

When I create script for ammonite 2.11 that has one or two @ then it is not imported properly. For example: ``` import coursier.MavenRepository interp.repositories() ++= Seq( MavenRepository("https://dl.bintray.com/denigma/denigma-releases"), MavenRepository("https://dl.bintray.com/comp-bio-aging/main/"), MavenRepository("https://oss.sonatype.org/content/repositories/releases")...

I constantly get [32m] when I use PPrint (OS == Linux Mint). How to get rid of it?

Cannot build with sbt

16

When I try to build with sbt I get: Project loading failed: (r)etry, (q)uit, (l)ast, or (i)gnore? r error: error while loading CharSequence, class file '/usr/lib/jvm/java-8-oracle/jre/lib/rt.jar(java/lang/CharSequence.class)' is broken (bad constant...