Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

ubuntu base update, Blast+ update, Soundex #3

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

ubuntu base update, Blast+ update, Soundex #3

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 5 additions & 2 deletions dockerfiles/nf-repeatmasking/Dockerfile
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
FROM ubuntu:14.04
FROM ubuntu:16.04

MAINTAINER Rob Syme <[email protected]>

Expand Down Expand Up @@ -39,7 +39,7 @@ RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/rmblast/2.2.28/ncbi-rmblas
rm -rf ncbi-rmblastn

# Install Blast+
RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-x64-linux.tar.gz && \
RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7.1/ncbi-blast-2.7.1+-x64-linux.tar.gz && \
tar -xzvf ncbi-blast* && \
find ncbi-blast* -type f -executable -exec mv {} bin \; && \
rm -rf ncbi-blast*
Expand Down Expand Up @@ -125,6 +125,9 @@ RUN apt-get install -qqy genometools bioperl
# Install Aragon
RUN apt-get install -qqy aragorn

# This needs to be done in order for RepeatMasker to run
RUN cpan Text::Soundex

# I can't bundle the girinst RepBase libraries with the docker image,
# so you'll need to get them yourself. Download them from
# http://www.girinst.org/server/RepBase/protected/repeatmaskerlibraries/RepBaseRepeatMaskerEdition-20170127.tar.gz
Expand Down