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vcftools vcf-merge error: tabix not found #172

Closed buchanae closed 6 years ago

buchanae commented 7 years ago

docker run -v pwd:/data biocontainers/vcftools:latest vcf-merge data/muse.normalized.vcf data/somaticsniper.normalized.vcf data/varscan.snp.normalized.vcf data/radia.normalized.vcf Unable to find image 'biocontainers/vcftools:latest' locally latest: Pulling from biocontainers/vcftools c62795f78da9: Already exists d4fceeeb758e: Already exists 5c9125a401ae: Already exists 0062f774e994: Already exists 6b33fd031fac: Already exists 7a5724671bcc: Already exists aa65e16b8de6: Already exists baa42fddbf04: Already exists 51705efff363: Already exists 46c05ebab1c2: Already exists 0b016b186f2b: Already exists 5b3a6e3318e6: Already exists da00ecd26c95: Already exists ec716ccd774c: Already exists 9572d4ef95b4: Already exists fb7f38888cd9: Already exists 4bb2d3630bbb: Pull complete Digest: sha256:c9f2300ee4d9c53cf738987d1dc791f22a5683401df52f5467141e4f57413964 Status: Downloaded newer image for biocontainers/vcftools:latest sh: 1: tabix: not found The command "tabix" not found, please add it to your PATH

at /usr/local/share/perl/5.22.1/Vcf.pm line 172. Vcf::throw(Vcf4_2=HASH(0x1242e00), "The command \"tabix\" not found, please add it to your PATH\x{a}") called at /usr/local/share/perl/5.22.1/Vcf.pm line 2672 VcfReader::get_chromosomes(Vcf4_2=HASH(0x1242e00)) called at /usr/local/bin/vcf-merge line 197 main::init_cols(HASH(0x16e37e0), Vcf4_2=HASH(0x16447a0)) called at /usr/local/bin/vcf-merge line 279 main::merge_vcf_files(HASH(0x16e37e0)) called at /usr/local/bin/vcf-merge line 12

osallou commented 6 years ago

tabix package is missing in container

osallou commented 6 years ago

could you just test install tabix package and container and checking it is ok before with fix the container? copy your input files in /tmp (to avoid files creation as root in your current directory) and:

docker run -it --rm --user root -v /tmp:/data biocontainers/vcftools:latest /bin/bash
# apt-get install tabix
# vcf-merge .....

thanks