search

10XGenomics / vartrix

Single-Cell Genotyping Tool
MIT License
185 stars 27 forks source link

pre-compiled binaries #39

Closed igordot closed 4 years ago

igordot commented 4 years ago

I noticed that the tool is still being actively developed, but releases stopped. I am mostly concerned about the pre-compiled binaries. Will those still be regularly released?

pmarks commented 4 years ago

@igordot we are working on a better Github actions-based binary build setup. Should have it available in the next week or so. What platforms would you like to run on? If Linux, what distro and version are you running?

igordot commented 4 years ago

I am on Red Hat Enterprise Linux Server 7.4.

Looking forward to the upcoming updates.

jfx319 commented 4 years ago

Looks like this issue of automatically compiling binaries is resolved, with the recent github-actions.

However, this change also broke GLIBC backwards compatibility between the manually released binary v1.1.8 and the automated release binary v1.1.13. The prior release was happy with GLIBC_2.17, but the new one seems to want GLIBC_2.18.

The 10xGenomics os support page linked to by the README on 10xgenomics/vartrix says OS support is compatible with linux kernel 3.10 and GBU libc 2.17, the newest v1.1.13 binary release complains that GLIBC_2.18 is not available. Is it possible to make this binary backwards compatible with the other libc versions listed on the main 10x support page? If not, that's okay; can always revert switch to a container. 

wget https://github.com/10XGenomics/vartrix/releases/download/v1.1.13/vartrix_linux
chmod u+x vartrix_linux
./vartrix_linux
# /lib64/libc.so.6: version `GLIBC_2.18' not found (required by ./vartrix_linux)

uname -r
# 3.10.0-957.27.2.el7.x86_64

ldd --version
# ldd (GNU libc) 2.17

versus

wget https://github.com/10XGenomics/vartrix/releases/download/v1.1.8/vartrix_linux
chmod u+x vartrix_linux
./vartrix_linux
# error: The following required arguments were not provided:
#     --bam <FILE>
#    --cell-barcodes <FILE>
#    --fasta <FILE>
#    --vcf <FILE>
#
#USAGE:
#    vartrix_linux --bam <FILE> --bam-tag <bam_tag> --cell-barcodes <FILE> --fasta <FILE> --log-level <log_level> --mapq <INTEGER> --out-matrix <OUTPUT_FILE> --padding <INTEGER> --ref-matrix <OUTPUT_FILE> --scoring-method <scoring_method> --threads <INTEGER> --valid-chars <valid_chars> --vcf <FILE>
#
#For more information try --help
igordot commented 4 years ago

I am getting the same error. Would be great to have it compiled as v1.1.8.

pmarks commented 4 years ago

@igordot @jfx319 I've posted good backward compatible binaries here: https://github.com/10XGenomics/vartrix/releases/tag/v1.1.14

The should work back to CentOS 6 and Ubuntu 12.04, or any other distro with GLIBC at least that recent. We're still working on generating & posting these automatically, but I'll post them manually till we have the worked out.

igordot commented 4 years ago

Thank you! I can confirm it works for me now.