Comments (8)
Hi. You can get reapear here: https://www.ebi.ac.uk/research/enright/software/kraken
I'll add it to the requirements documentation.
from umi-tools_pipelines.
Thanks, I was able to install reaper from the link you posted.
I ran into another issue though, CGAT
is also listed as a requirement, but the repository appears to be archived, and there is no release 0.2.4
. When I try to run the pipelines I get
Traceback (most recent call last):
File "../UMI-tools_pipelines/pipeline_scRNASeq.py", line 83, in <module>
import CGAT.Experiment as E
ImportError: No module named CGAT.Experiment
Do you have any suggestions on how to install the correct version of the CGAT module?
from umi-tools_pipelines.
The best course of action here probably depends on what your aim is. If you are undertaking a reproducibility excercise, then the code for this particular version is here:
https://github.com/CGATOxford/cgat/tree/v0.2.4
You are also going to need from https://github.com/CGATOxford/CGATPipelines (the commit has is in the requirements)
However, I don't know how well the installation procedures will work.
So, if you are just interested in reproducing the results, rather then testing how reproducible the code is, then I recommend you install the modern versions. You will need cgat-apps
which is installable from bioconda
and cgat-flow
which you can get from here:
https://github.com/cgat-developers/cgat-flow
cgat-flow
has an installation script which will build the a conda envirnoment to run it in. However, I tend to do it manually by cloning the repo and typing
mamba env create -f conda/environments/cgat-flow-pipelines.yml -p /PATH/TO/LOCATION/FOR/ENV
activating the environment
source activate /PATH/TO/LOCATION/FOR/ENV
then running python setup.py develop
If you take this path, the pipelines will need a little light refactoring, but I can probably help with that once exam season is over.
from umi-tools_pipelines.
The background for my request is that I have developed a reference-free umi deduplication tool, and I would like to compare it's results against UMI-tools. I've been trying to install the original versions in a conda environment, but it appears they are too old to easily install.
Would you recommend I use the latest version of cgat-apps
and cgat-flow
, and then run the UMI-tools_pipelines in that environment?
from umi-tools_pipelines.
Yes, that is probably the best way. Some things have changed in the API since 2015. CGAT
was split into cgat
and cgatcore
. Several of the modules now have lowercase names e.g. experiment
rather than Experiment
and pipeline
rather than Pipeline
, and most CamelCase names are now underscore_names (e.g. openFile
is now open_file
), but its not too difficult a transition and installation is loads easier.
from umi-tools_pipelines.
@IanSudbery I've been refactoring the pipeline to work with the latest versions of cgat
, but I'm stuck on report section of the pipeline (P.run_report
and P.publish_report
, see here) which do not appear to exist. Has this functionality removed from the latest version? If so, do you have any guidance on what these task should do, and how to replicate this in the latest version?
from umi-tools_pipelines.
from umi-tools_pipelines.
@IanSudbery
I've made a start with refactoring (see here), but I'm having a hard time installing all required tools in a single conda environment, especially since some of the old cgat code the pipelines rely on is still on python 2. Do you have time to take a look at creating a conda environment that can run these pipelines?
from umi-tools_pipelines.
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