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chhylp123 / BitMapperBS

BitMapperBS: a fast and accurate read aligner for whole-genome bisulfite sequencing
Apache License 2.0
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docker container #7

Closed antonkulaga closed 5 years ago

antonkulaga commented 5 years ago

I've made a docker container to run BitMapperBS in bioinformatic pipelinies, currently it is avaliable at docker pull quay.io/comp-bio-aging/bit_mapper_bs (container) and https://github.com/antonkulaga/biocontainers/tree/master/BitMapperBS (sources). If needed I can adapt it for inclusion into official BitMapperBS repo

chhylp123 commented 5 years ago

Hi antonkulaga,

Many thanks for your work! I'm very happy to merge your work into BitMapperBS. May I ask what should I do for this?

antonkulaga commented 5 years ago

Sorry for the delay in response - was overloaded. I am currently having issues with 

libhts.so.2to3part2: cannot open shared object file: No such file or directory

even though I had no issues when compiling. @chhylp123 maybe you can suggest how to fix it? even though I did not have any build errors on this :(

chhylp123 commented 5 years ago

Sorry for the delay in response - was overloaded. I am currently having issues with

libhts.so.2to3part2: cannot open shared object file: No such file or directory

even though I had no issues when compiling. @chhylp123 maybe you can suggest how to fix it? even though I did not have any build errors on this :(

This is because BitMapperBS cannot find shared libraries of htslib. The shared libraries of htslib is saved on "BitMapperBS-master/htslib_aim" in default. I guess you copied the binaries "bitmapperBS" and "pscan" to another directory, but did not copy "htslib_aim". So if you want to copy bitmapperBS to another directory (for example "new_dir"), you must try the following command:

cp -a BitMapperBS-master/bitmapperBS new_dir
cp -a BitMapperBS-master/psascan new_dir
cp -a BitMapperBS-master/htslib_aim new_dir

Another solution is try:

ldd BitMapperBS-master/bitmapperBS

at the origin directory "BitMapperBS-master". And then you can find where shared libraries should be.

chhylp123 commented 5 years ago

Sorry for the delay in response - was overloaded. I am currently having issues with

libhts.so.2to3part2: cannot open shared object file: No such file or directory

even though I had no issues when compiling. @chhylp123 maybe you can suggest how to fix it? even though I did not have any build errors on this :(

Hi antonkulaga,

is this problem solved?

antonkulaga commented 5 years ago

@chhylp123 I solved the libhts.so issue, but now I have the overflow problem:

*** buffer overflow detected ***: /opt/BitMapperBS/bitmapperBS terminated
16 Aborted                 (core dumped) /data/indexes/HUMAN/29/GRCh38.primary_assembly.genome.fa

when I run it with docker it looks as following:

docker run -v /data:/data quay.io/comp-bio-aging/bit_mapper_bs:latest /opt/BitMapperBS/bitmapperBS --index /data/indexes/HUMAN/29/GRCh38.primary_assembly.genome.fa

You can download the primary assembly file from https://www.gencodegenes.org/human/

P.S. Noticed that is crashes this way only part of the time

antonkulaga commented 5 years ago

Basically, I want to make a PR for docker container as soon as I will be sure that it works well in my pipelines.

chhylp123 commented 5 years ago

@chhylp123 I solved the libhts.so issue, but now I have the overflow problem:

*** buffer overflow detected ***: /opt/BitMapperBS/bitmapperBS terminated
16 Aborted                 (core dumped) /data/indexes/HUMAN/29/GRCh38.primary_assembly.genome.fa

when I run it with docker it looks as following:

docker run -v /data:/data quay.io/comp-bio-aging/bit_mapper_bs:latest /opt/BitMapperBS/bitmapperBS --index /data/indexes/HUMAN/29/GRCh38.primary_assembly.genome.fa

You can download the primary assembly file from https://www.gencodegenes.org/human/

P.S. Noticed that is crashes this way only part of the time

So you mean bitmapperbs can run sucessfully sometimes, and crashed sometimes?

antonkulaga commented 5 years ago

Making a PullRequest https://github.com/chhylp123/BitMapperBS/pull/10

chhylp123 commented 5 years ago

Making a PullRequest #10

I have merged it. Thank you very much.

antonkulaga commented 5 years ago

Consider to be fixed

xie186 commented 5 years ago

@antonkulaga Is it possible that you can write an example of how to use the docker image? Thanks in advance.