installation

[Kishor Kumar Sarker]

Hi,
I am trying to install trinity using conda. I have used the following cmdline:
conda install -c bioconda trinity

But the version seems a bit older (v2.1.1). And this version is not
suitable for my analysis design since there is no parameter like:
'--sample_files'. I have tried to update like:
conda install -c bioconda trinity=2.15.1

But I faced issues like:
Collecting package metadata (current_repodata.json): done
Solving environment: unsuccessful initial attempt using frozen solve.
Retrying with flexible solve.
Solving environment: unsuccessful attempt using repodata from
current_repodata.json, retrying with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: unsuccessful initial attempt using frozen solve.
Retrying with flexible solve.
Solving environment: \
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found to be
incompatible with each other:

Output in format: Requested package -> Available versionsThe following
specifications were found to be incompatible with your system:

- feature:/linux-64::__glibc==2.35=0
- python=3.9 -> libgcc-ng[version='>=11.2.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.35


how to solve that? update the glibc version? or python?



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With best regards,

Kishor Kumar Sarker

PostDoc Fellow
Lab of Molecular Systematics and Ecology
Faculty of Life Sciences
Shanghai Ocean University, Shanghai, China
Phone: +8618621974360

[Brian Haas]

Hi,

Please use the singularity image when running Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-in-Docker#running-trinity-using-singularity

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Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas

 

[Brian Haas]

Hi,

For the singularity installation, try this assuming linux:

https://docs.sylabs.io/guides/3.0/user-guide/installation.html#install-the-debian-ubuntu-package-using-apt