search

jason-weirather / AlignQC

Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser compatible xhtml to visualize/share/store/extract analysis results.
Apache License 2.0
45 stars 10 forks source link

problem with the installation via Conda #26

Open shaghayeghsoudi opened 1 year ago

shaghayeghsoudi commented 1 year ago

Hi, thanks for developing such a nice package. I just started learning how it works and wanted to run some tests on my both PacBio and ONT reads. But I fail to install via conda. I am not sure if this is something related to the tool or just related to my conda? Obviously I do not have issue installing other packages or new environments though. This is my installation command: conda create -n alignqc -c vacation AlignQC when it starts solving the environment, it fails by getting solving environment killed . I appreciate if you could let me know in case there is something that I can do to get this installed via conda. Thanks

jason-weirather commented 1 year ago

Hi Shagheyegh, Sorry for the conda troubles, my best suggestion is to try the docker container if you are able:

Sorry for the issues with the conda environment. Its quite an old package, so I would recommend executing through the docker if you are able.

Example

$ docker pull vacation/alignqc:2.0.5
$ docker run -u $(id -u):$(id -g) -v $(pwd)/example_data/:$(pwd)/example_data/ vacation/alignqc:2.0.5 alignqc analyze -g $(pwd)/example_data/chr21chr22chrM.fa.gz -t $(pwd)/example_data/chr21chr22chrM.gencode25.gtf.gz $(pwd)/example_data/chr21chr22chrM.bam -o $(pwd)/example_data/myoutput.xhtml

Docker hub link: vacation/alignqc:2.0.5