Closed charlesreid1 closed 5 years ago
Running the same conda env create
command on a stock copy of elvers still fails on the same errors (not finding versions of python 3.6 or python 3.7 in the environment), so these errors are not specifically related to pinning the version numbers in the environment.yml file (except trinity, which works fine if no version number is specified in its environment.yml file).
Should the environment.yml files be specifying a version of python to use?
just checking - are you working in the base elvers-env
environment?
Ah, thank you! I was forgetting the initial environment setup using the top-level environment.yml file. Doing a
conda env create --file environment.yml -n elvers-env
as per the Quickstart fixed the problem.
Actually, sourmash 2.0 requires python 3.7, and the top level elvers environment.yml specifies python 3.6 or higher, so not quite solved yet.
I will leave it up to you whether to bump the python version in the elvers environment.yml or roll back the sourmash version - just let me know and close this issue and I'll make the change in PR #136.
hm, I say bump the version as long as it doesn't screw up dammit, which currently requires python 3.6
Okay, slight revision, since we're specifying python 3.6 or greater, this means that when we create an environment with sourmash, which requires python 3.7, conda will simply download and install python 3.7, so we don't need to bump the python version in the top-level environment.yml file:
$ conda env create --file elvers/rules/sourmash/environment.yml -n sourmash_test
Solving environment: done
Downloading and Extracting Packages
harfbuzz-2.4.0 | 1.5 MB | ######################################################################### | 100%
wheel-0.33.1 | 34 KB | ######################################################################### | 100%
pyparsing-2.4.0 | 55 KB | ######################################################################### | 100%
sip-4.18.1 | 277 KB | ######################################################################### | 100%
matplotlib-base-3.0. | 6.6 MB | ######################################################################### | 100%
sourmash-2.0.0 | 262 KB | ######################################################################### | 100%
liblapack-3.8.0 | 6 KB | ######################################################################### | 100%
openblas-0.3.5 | 15.8 MB | ######################################################################### | 100%
gdk-pixbuf-2.32.2 | 759 KB | ######################################################################### | 100%
pango-1.40.14 | 524 KB | ######################################################################### | 100%
glib-2.58.3 | 3.3 MB | ######################################################################### | 100%
setuptools-41.0.0 | 635 KB | ######################################################################### | 100%
certifi-2019.3.9 | 149 KB | ######################################################################### | 100%
ijson-2.3 | 13 KB | ######################################################################### | 100%
pip-19.0.3 | 1.8 MB | ######################################################################### | 100%
cairo-1.16.0 | 1.5 MB | ######################################################################### | 100%
python-dateutil-2.8. | 219 KB | ######################################################################### | 100%
python-3.7.1 | 36.4 MB | #########3
Will close this and continue to post info about what's going on in PR #136.
I am trying to pin version numbers in the environment.yml files. But when I double-check that the environments work by running the command
I run into some problems with the following software:
All due to various issues (python not being found, mismatched python version, specified software version can't be found, etc.)
I will include the output of the above command running with unmodified environment.yml files and check to make sure those are all okay and that this is not an issue with my conda setup.
Output included below.
bowtie works:
dammit does not work:
deseq2 works:
edgeR works:
fastqc works:
khmer does not work:
multiqc does not work:
paladin works:
pear works:
plass works:
rcorrector works:
salmon works:
sourmash does not work:
trimmomatic works:
trinity does not work: