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humanlongevity / HLA

xHLA: Fast and accurate HLA typing from short read sequence data
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Unable to compile xHLA #6

Open dhwani2410 opened 7 years ago

dhwani2410 commented 7 years ago

dhwani@dhwani-Precision-WorkStation-T7500:~/Documents/hla_scan/test_out/HLA-master/docker$ make build docker build -t docker-dev.hli.io/xchao/hla-dev -f dev.dockerfile . flag provided but not defined: -f

Usage: docker build [OPTIONS] PATH | URL | -

Build a new container image from the source code at PATH

-q=false: Suppress verbose build output -t="": Tag to be applied to the resulting image in case of success docker tag docker-dev.hli.io/xchao/hla-dev docker-dev.hli.io/xchao/hla-dev:0.0.0 2017/07/17 10:35:27 dial unix /var/run/docker.sock: permission denied make: *** [build] Error 1

tanghaibao commented 7 years ago

@dhwnai2410 it may be that your docker version is too low. What's the output of docker -v? It might be worthwhile to upgrade to the latest version.

dhwani2410 commented 7 years ago

version .0.5.3

tanghaibao commented 7 years ago

@dhwnai2410 this is an outdated version. Would you mind trying to upgrade docker to a more recent version?

dhwani2410 commented 7 years ago

anurag@anurag-Precision-WorkStation-T5400:~/Downloads/HLA-master/docker$ sudo make build [sudo] password for anurag: Sorry, try again. [sudo] password for anurag: docker build -t docker-dev.hli.io/xchao/hla-dev -f dev.dockerfile . Sending build context to Docker daemon 17.92 kB Step 1 : FROM ubuntu:14.04 14.04: Pulling from library/ubuntu

cb56c90f0b30: Pull complete 0acc551e5716: Pull complete 8956dcd35143: Pull complete 908242721214: Pull complete b44ff14dd3bb: Pull complete Digest: sha256:5faf6cb681da2be979a177b60d8c18497f962e3d82268c49db6c74008d0c294d Status: Downloaded newer image for ubuntu:14.04 ---> 4a2820e686c4 Step 2 : RUN sudo sh -c 'echo "deb http://cran.rstudio.com/bin/linux/ubuntu trusty/" >> /etc/apt/sources.list' && gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9 && gpg -a --export E084DAB9 | sudo apt-key add - ---> Running in b30541f46944 gpg: directory /root/.gnupg' created gpg: new configuration file/root/.gnupg/gpg.conf' created gpg: WARNING: options in /root/.gnupg/gpg.conf' are not yet active during this run gpg: keyring/root/.gnupg/secring.gpg' created gpg: keyring `/root/.gnupg/pubring.gpg' created gpg: requesting key E084DAB9 from hkp server keyserver.ubuntu.com gpg: keyserver timed out gpg: keyserver receive failed: keyserver error The command '/bin/sh -c sudo sh -c 'echo "deb http://cran.rstudio.com/bin/linux/ubuntu trusty/" >> /etc/apt/sources.list' && gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9 && gpg -a --export E084DAB9 | sudo apt-key add -' returned a non-zero code: 2 Makefile:6: recipe for target 'build' failed make: *** [build] Error 2

dhwani2410 commented 7 years ago

Client: Version: 1.12.6 API version: 1.24 Go version: go1.6.2 Git commit: 78d1802 Built: Tue Jan 31 23:35:14 2017

tanghaibao commented 7 years ago

Not sure why the compile failed. It works for me and other users. I have pushed a compiled image tanghaibao/hla. Would you test it out?

docker pull tanghaibao/hla
docker run -v `pwd`:`pwd` -w `pwd` tanghaibao/hla \
    --sample_id test --input_bam_path test.bam \
    --output_path test
dhwani2410 commented 7 years ago

anurag@anurag-Precision-WorkStation-T5400:~/Desktop/dhwani$ sudo docker run -v pwd:pwd -w pwd tanghaibao/hla --sample_id test --input_bam_path abc_hg38.bam --output_path test [23/Jul/2017 03:49:40] INFO - Xie Chao's HLA typing algorithm [23/Jul/2017 03:49:40] INFO - Sample_id: test Input file: abc_hg38.bam Extracting reads from S3 skipped 7306 duplicated reads Aligning reads to IMGT database processing FASTQ file found 35475 reads processing MSA file found 26381 HLA exons processing FASTQ file Error: Invalid input file format matched to 0 HLA exons 0 reads matched to HLA types not in the MSA file translating matches to MSA Typing Error in fread(align.path) : File is empty: hla-test/test.tsv Execution halted Traceback (most recent call last): File "/opt/bin/run.py", line 57, in check_call([bin_path, args.input_bam_path, args.sample_id]) File "/usr/lib/python2.7/subprocess.py", line 540, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/opt/bin/typer.sh', 'abc_hg38.bam', 'test']' returned non-zero exit status 1