Problem with installation

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mette Joergensen

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Jan 9, 2023, 4:43:51 AM1/9/23
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Hi 
I'm trying to install NGLess on CentOS Linux release 7.8.2003 using Bioconda.
I did 
>conda install -c bioconda ngless

Everything seemed to work, but when I tried to run NGLEss I got the following error.

/usr/local/bin/ngless: line 9: /bin/ngless-wrapped: No such file or directory

Any idea what can be wrong ?
Best,
Mette

Luis Pedro Coelho

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Jan 9, 2023, 4:51:25 AM1/9/23
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Perhaps you are not running this inside the conda environment?

conda create -n ngless-env
conda activate ngless-env

conda install -c conda-forge -c bioconda ngless
ngless ...

should work

and you can activate the environment later with conda activate ngless-env


Best
Luis

Luis Pedro Coelho | Fudan University | https://luispedro.org

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mette Joergensen

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Jan 9, 2023, 5:29:56 AM1/9/23
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Thanks Luis for the quick reply
It seems to be working.

What I'm actually trying to do is to build a docker image including NGLess and my own NGLess modules..My current Dockerfile look like this 
--------
# CentOS Linux release 7.8.2003 The same as Computerome
FROM conda/miniconda3-centos7

# Make a work folder that will be a root folder
WORKDIR /dockerWorkDir

#update conda
RUN conda update -n base -c defaults conda && \
# Install NGLess
    conda init bash && \
    source ~/.bash_profile && \
    source ~/.bashrc && \
    conda create -n ngless-env && \
    conda activate ngless-env && \

    conda install -c conda-forge -c bioconda ngless
---------

But it seems like the users will need to reactive the ngless-env before ngless is working in the Docker. Is there any way to avoid this ?
 


Luis Pedro Coelho

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Jan 9, 2023, 4:14:17 PM1/9/23
to mette Joergensen, NGLess List
Hi Mette,

A few possible solutions:

1 (easiest, probably slow). Just install the following binary into your environment


The reason this may be slow is that dependencies are built in a very non-optimized way for complex reasons.

2 (still easy). Install all the dependencies (megahit, samtools, bwa) separately and then install


This is, in fact, how the conda package works 

3 (not so easy, probably the most dockery way). Install all the dependencies. Add haskellstack and build NGLess from scratch

4 (no idea, I'm not that fluent in docker). Use this prebuilt docker image and add your things?


HTH
Luis

Luis Pedro Coelho | Fudan University | https://luispedro.org


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