search

xjtu-omics / msisensor-pro

Microsatellite Instability (MSI) detection using high-throughput sequencing data.
Other
93 stars 20 forks source link

docker image has error while loading libraries #23

Open anoronh4 opened 3 years ago

anoronh4 commented 3 years ago

I am trying to run msisensor using the dockerhub image pengjia1110/msisensor-pro:latest. i am running with singularity v 3.3.0 and getting the following error:

$ singularity exec ./msisensor-pro_latest.sif msisensor-pro
msisensor-pro: error while loading shared libraries: libhts.so.3: cannot open shared object file: No such file or directory

i get this error regardless of whether i use the singularity option -e for a clean environment. maybe something is missing in the container because it was present in the host environment during testing?

PengJia6 commented 3 years ago

@anoronh4 Sorry for the late reply. We just test the msisensor-pro with docker. It seems htslib is missed in the container, but I do not meet this in docker. I will test it in singularity and give you a feedback as soon as possible.

sscien commented 2 years ago

Hi Peng, have you resolved this htslib issue?

PengJia6 commented 2 years ago

@sscien Sorry, I can not install singularity version in our HPC, but the conda and docker version is OK.

iranmdl commented 2 years ago

Hi! @PengJia6 I am having the same issue when converting docker image to singularity (unfortunately I cannot use docker or conda). Any updates on this?

iranmdl commented 2 years ago

If anyone is experiencing the same issue, it can be fixed by modifying the dockerfile in the following way:

RUN cd /tmp \
  && git clone https://github.com/xjtu-omics/msisensor-pro.git \
  && cd msisensor-pro \
  && ./INSTALL \
  && cp -r /tmp/msisensor-pro/binary/msisensor-pro /usr/bin/ \
  && cp -r /tmp/msisensor-pro/vendor/htslib-1.11 /usr/lib

ENV LD_LIBRARY_PATH /usr/lib/htslib-1.11/

Then, convert the docker image to singularity and run it with: singularity exec -C msisensorpro_fixed.sif msisensor-pro cc. @PengJia6

PengJia6 commented 2 years ago

@iranmdl Thanks for your contributions！ I will test and update the dockerfile.

oliverartz commented 1 year ago

Hi @PengJia6, did you end up fixing the docker? I am running into the same issues as @anoronh4. Is there a solution for this?

gudeqing commented 5 months ago

I also got this same issue using the latest image using cwltool, and the reason is that the “/tmp” directory is replaced by cwltool