Building Docker image fails

KleinSamuel commented 2 months ago

Hello,

when building the Docker image I get the following error.

Steps to reproduce:

wget https://github.com/AlgoLab/galig/releases/tag/v1.1.7
tar xzvf galig-1.1.7.tar.gz
cd galig-1.1.7/docker/
docker build -t galig .

Part of the log:

[...]
STEP 10/16: RUN git clone --depth=1 --recursive https://github.com/AlgoLab/galig.git
Cloning into 'galig'...
--> 838ce15143da
STEP 11/16: RUN cd galig ; make prerequisites
make[1]: *** No rule to make target 'prerequisites'.  Stop.
make: *** [target.mk:17: /galig/obj] Error 2
Error: building at STEP "RUN cd galig ; make prerequisites": while running runtime: exit status 2

Do I need to use a specific version/tag for this to work?

KleinSamuel commented 2 months ago

ldenti commented 2 months ago

I think this is now solved as well.

Just a bit more of info: we had to make some changes to compilation in order to publish asgal in bioconda. This broke something. But anyway it is safe to use v1.1.7. In the meantime, we will try to fix the Dockerfile to use the latest version.

Thanks again!

ldenti commented 2 months ago

In any case, if you want to use docker and v1.1.8, you can use the biocontainer created by conda (thanks @yp for pointing this out):

docker pull quay.io/biocontainers/asgal:1.1.8--h43eeafb_1
docker run -it quay.io/biocontainers/asgal:1.1.8--h43eeafb_1 /bin/bash
/usr/local/bin/asgal --help
# this to list all binaries
ls /usr/local/bin/SpliceAwareAligner /usr/local/bin/asgal_*

AlgoLab / galig

Building Docker image fails #23