Open avp65 opened 3 weeks ago
Hi, it's quite painful to install these dependencies, so I'd recommend just use the prebuilt docker image
Hi thank you for your response. Can you explain me how to find and use the prebuilt docker image? I thought we have to use the file named Dockerfile to built it by ourselve that's why I run the command line: docker build . -f Dockerfile.txt. Sorry for my question, I begin in this field and I never used this way to run a tool.
In the readme there's example commands that start with 'docker run'
On Mon, 24 June 2024, 6:05 pm avp65, @.***> wrote:
Hi thank you for your response. Can you explain me how to find and use the prebuilt docker image? I thought we have to use the file named Dockerfile to built it by ourselve that's why I run the command line: docker build . -f Dockerfile.txt.
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Readme has errors, try:
docker pull mrbradley2/clinsv:v1.0
not the readme's
docker pull mrbradley2/clinsv:v1.0.0
Thank you for your response, I tried it but it stops prematurely with this message :
***** error exist status != 0 (35072), please check /app/project_folder/alignments/FR05812606/bw/sh/bigwig.q0.FR05812606.e for more information
(base) av65@ml22-1 ClinSV_test % docker pull mrbradley2/clinsv:v1.0
refdata_path=$PWD/clinsv/refdata-b38
input_path=$PWD
project_folder=$PWD/test_run
docker run -v $refdata_path:/app/ref-data \
-v $project_folder:/app/project_folder \
-v $input_path:/app/input \
--entrypoint "perl" mrbradley2/clinsv:v1.0 /app/clinsv/bin/clinsv \
-r all \
-p /app/project_folder/ \
-i "/app/input/*.bam" \
-ref /app/ref-data/refdata-b38 \
v1.0: Pulling from mrbradley2/clinsv
Digest: sha256:17a0eae080654a21a74d1cd43b1c5f35dfcf57f99003ef9d77b46cad6acc0b0a
Status: Image is up to date for mrbradley2/clinsv:v1.0
docker.io/mrbradley2/clinsv:v1.0
What's Next?
1. Sign in to your Docker account → docker login
2. View a summary of image vulnerabilities and recommendations → docker scout quickview mrbradley2/clinsv:v1.0
WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
### executing: sh /app/project_folder/alignments/FR05812606/bw/sh/bigwig.createWigs.FR05812606.sh &> /app/project_folder/alignments/FR05812606/bw/sh/bigwig.createWigs.FR05812606.e ...
##############################################
#### ClinSV ####
##############################################
# 28/06/2024 23:11:26
# clinsv dir: /app/clinsv
# projectDir: /app/project_folder
# sampleInfoFile: /app/project_folder/sampleInfo.txt
# name stem: project_folder
# lumpyBatchSize: 5
# genome reference: /app/ref-data/refdata-b38
# run steps: all
# number input bams: 1
# Read Sample Info from /app/project_folder/sampleInfo.txt
# use: FR05812606 H7LH3CCXX_6 /app/input/NA12878.grch38.subsampled.bam
# 1 samples to process
# If not, please exit make a copy of sampleInfo.txt, modify it and rerun with -s sampleInfo_mod.txt pointing to the new sample info file.
###### Generate the commands and scripts ######
# bigwig
# lumpy
# cnvnator
# annotate
# prioritize
# qc
###### Run jobs ######
### finished after (hh:mm:ss): 06:16:34
### exist status: 0
### executing: sh /app/project_folder/alignments/FR05812606/bw/sh/bigwig.q0.FR05812606.sh &> /app/project_folder/alignments/FR05812606/bw/sh/bigwig.q0.FR05812606.e ...
### finished after (hh:mm:ss): 00:17:26
### exist status: 35072
***** error exist status != 0 (35072), please check /app/project_folder/alignments/FR05812606/bw/sh/bigwig.q0.FR05812606.e for more information
Below is what is in the file
+ export PATH=/app/clinsv/bin:/app/clinsv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ PATH=/app/clinsv/bin:/app/clinsv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ cd /app/project_folder/alignments/FR05812606/bw/
+ wigToBigWig /app/project_folder/alignments/FR05812606/bw/tmp/FR05812606.q0.wig /app/ref-data/refdata-b38/genome/Homo_sapiens_assembly38.fasta.chrom.sizes /app/project_folder/alignments/FR05812606/bw/FR05812606.q0.bw
/app/project_folder/alignments/FR05812606/bw/sh/bigwig.q0.FR05812606.sh: line 7: 14088 Killed wigToBigWig /app/project_folder/alignments/FR05812606/bw/tmp/FR05812606.q0.wig /app/ref-data/refdata-b38/genome/Homo_sapiens_assembly38.fasta.chrom.sizes /app/project_folder/alignments/FR05812606/bw/FR05812606.q0.bw
Hello
I am a beginner in bioinformatic and the use of command line tools. I am trying to build the image docker using the Dockerfile. The process failed at that step :
RUN cd $clinsv_path && \ git clone --branch latest-stable https://github.com/root-project/root.git root_src && \ mkdir root_build root_install && cd root_build && \ cmake -DCMAKE_INSTALL_PREFIX=../root_install ../root_src && \
Here is a copy of all the process and the error message that I got. What should I do to solve this problems ? Thank you.