Open IanSudbery opened 3 years ago
However, if I force upgrate cgat-apps
to 0.6.0 and force downgrade pysam to 0.15.2, it works.
Or it does in some envs.
on other attempts, it seems that pysam 0.9.1 gets isntalled, and its impossible to shift it off that.
This is at least partially because conda is not respecting the pysam pin in cgat-flow-pipelines.yml
. Or at least, it respects it when you update
with cgat-flow-pipelines.yml
but it doesn't stay pinned, because its not being installed as a dependency of something, just as a request in its own right. I suggest we make it a pinned dependency of cgat-apps.
On my last installation attempt, I combined all three ymls (cgat-flow.yml
, cgat-flow-pipelines.yml
and pipelines-extra.yml
) into a single yml
, removed duplicates, added cgat-apps
to the list, and the installation went fine, and was much easier.
Related to #143, and may have already been partly addressed by #153. It may already be possible to close this now that pysam unpinned, but if not, then rpy2 unpin would almost certainly fix this.
If I create a new environment containing only cgat-apps then the following works fine:
If I then update the environment to install the cgat-flow dependencies
this now errors:
I notice that during installation
cgat-apps
is downgraded from v0.6.0 to v0.5.4 and pysam is upgraded from 0.15.2 to 0.16.0.Now I update with
cgat-flow-pipelines.yml
.I notice that pysam is downgraded again to 0.15.2.
Errror message the same.
Then I install
pipelines-extra.yml
. Version of pysam is changed AGAIN. This time to 0.15.3.Still get the same error.