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nextflow-io / patterns

A curated collection of Nextflow implementation patterns
http://nextflow-io.github.io/patterns/
MIT License
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Dockerfile refers to non-existing file #1

Closed huguesfontenelle closed 9 years ago

huguesfontenelle commented 9 years ago

bin/AMPA.pl does not exist in this examples repository, and $ docker build . fails.

$ docker build .
Sending build context to Docker daemon 6.546 MB
Step 0 : FROM pditommaso/dkrbase:1.1
 ---> ae4cb2b803ba
Step 1 : MAINTAINER Paolo Di Tommaso <paolo.ditommaso@gmail.com>
 ---> Using cache
 ---> 7f956c07387e
Step 2 : RUN apt-get install -q -y gnuplot python && apt-get clean
 ---> Using cache
 ---> 730aeb7ec1b6
Step 3 : RUN cpanm Math::CDF Math::Round &&   rm -rf /root/.cpanm/work/
 ---> Using cache
 ---> 1d85dd9a180e
Step 4 : RUN wget -q ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.29/ncbi-blast-2.2.29+-x64-linux.tar.gz &&     tar xf ncbi-blast-2.2.29+-x64-linux.tar.gz &&     mv ncbi-blast-2.2.29+ /opt/ &&     rm -rf ncbi-blast-2.2.29+-x64-linux.tar.gz &&     ln -s /opt/ncbi-blast-2.2.29+/ /opt/blast
 ---> Using cache
 ---> c8bfe75956a3
Step 5 : RUN wget -q http://tcoffee.org/Packages/Stable/Version_11.00.8cbe486/linux/T-COFFEE_installer_Version_11.00.8cbe486_linux_x64.tar.gz &&   tar xf T-COFFEE_installer_Version_11.00.8cbe486_linux_x64.tar.gz -C /opt &&   mv /opt/T-COFFEE_installer_Version_11.00.8cbe486_linux_x64 /opt/tcoffee &&   rm -rf /opt/tcoffee/plugins/linux/*  &&   rm T-COFFEE_installer_Version_11.00.8cbe486_linux_x64.tar.gz
 ---> Using cache
 ---> 5381d47ca2b9
Step 6 : ADD bin/AMPA.pl /usr/local/bin/
bin/AMPA.pl: no such file or directory

Temporary resolution: comment out in Dockerfile (?) or add the script found in another repository nextflow-io/tests/bin/AMPA.pl.

pditommaso commented 9 years ago

Thanks for reporting that. Actually that script is not used.