Closed hackdna closed 4 years ago
Thanks-- does getting 1.9 not work? 1.7 is super old.
Sure, this is just a quick fix to help folks with broken bcbio installations. According to https://github.com/bioconda/bioconda-recipes/issues/12100, samtools 1.9 had issues since 2018. I will test more recent versions and report back.
Tested successfully by bcbio_nextgen.py upgrade -u development --tools
with samtools=1.10
in tmpbcbio-install/cloudbiolinux/contrib/flavor/ngs_pipeline_minimal/packages-conda.yaml
:
vagrant@bcbio:~$ which samtools
/home/vagrant/local/share/bcbio/anaconda/bin/samtools
vagrant@bcbio:~$ samtools --version
samtools 1.10
Using htslib 1.10.2
Copyright (C) 2019 Genome Research Ltd.
vagrant@bcbio:~$ conda list openssl
# packages in environment at /home/vagrant/local/share/bcbio/anaconda:
#
# Name Version Build Channel
openssl 1.1.1g h516909a_1 conda-forge
pyopenssl 19.1.0 py36_0 conda-forge
r-openssl 1.4.1 r35he5c4762_0 conda-forge
Installing from scratch may be a different story because by default mamba/conda resolves samtools to version 1.7. However, I don't know an easy way to test that because bcbio install always overwrites tmpbcbio-install/cloudbiolinux
with a version from GitHub.
Heya, you can skip the cloudbiolinux update by linking tmpbcbio-install/cloudbiolinux
to your local one.
I did but this directory got overwritten with cloudbiolinux from GitHub when running bcbio_nextgen_install.py
.
Great, can you just push the 1.10 fix and we can see if it works, we can always revert it.
Thanks Ilya!
It worked for me:
vagrant@bcbio:~$ which samtools
/home/vagrant/local/share/bcbio/anaconda/bin/samtools
vagrant@bcbio:~$ samtools --version
samtools 1.10
Using htslib 1.10.2
Copyright (C) 2019 Genome Research Ltd.
vagrant@bcbio:~$ conda list openssl
# packages in environment at /home/vagrant/local/share/bcbio/anaconda:
#
# Name Version Build Channel
openssl 1.1.1g h516909a_1 conda-forge
pyopenssl 19.1.0 py36_0 conda-forge
r-openssl 1.4.1 r35he5c4762_0 conda-forge
Awesome, thanks so much. Worked for me too.
To fix https://github.com/bcbio/bcbio-nextgen/issues/3320 and toward https://github.com/bcbio/bcbio-nextgen/issues/3318
I performed a clean bcbio install using the latest master and ended up with the following working configuration:
This update will ensure this configuration is reproducible. Tested using:
bcbio_nextgen.py upgrade -u development --tools