Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
P
panacota
Manage
Activity
Members
Labels
Plan
Issues
Issue boards
Milestones
Code
Merge requests
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Snippets
Build
Pipelines
Jobs
Pipeline schedules
Artifacts
Deploy
Releases
Container registry
Model registry
Operate
Environments
Monitor
Incidents
Analyze
Value stream analytics
Contributor analytics
CI/CD analytics
Repository analytics
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
GitLab community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
Amandine PERRIN
panacota
Commits
c9e13fdf
Commit
c9e13fdf
authored
5 years ago
by
Amandine PERRIN
Browse files
Options
Downloads
Patches
Plain Diff
update blastp installation for prokka
parent
2b3a42dc
No related branches found
No related tags found
No related merge requests found
Pipeline
#23655
failed
5 years ago
Stage: build
Changes
1
Pipelines
1
Show whitespace changes
Inline
Side-by-side
Showing
1 changed file
for_tests/Dockerfile
+5
-3
5 additions, 3 deletions
for_tests/Dockerfile
with
5 additions
and
3 deletions
for_tests/Dockerfile
+
5
−
3
View file @
c9e13fdf
...
@@ -8,16 +8,17 @@ RUN apt-get update &&\
...
@@ -8,16 +8,17 @@ RUN apt-get update &&\
# Install packages needed and update pip
# Install packages needed and update pip
RUN
apt-get
install
-y
\
RUN
apt-get
install
-y
\
wget
\
wget
\
python3
-pip
\
python3
\
python3
python3
-pip
RUN
pip3
install
--upgrade
pip
RUN
pip3
install
--upgrade
pip
# Update makeblastdb for prokka
# Update makeblastdb
and blastp
for prokka
WORKDIR
/tmp
WORKDIR
/tmp
RUN
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.10.0+-x64-linux.tar.gz
&&
\
RUN
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.10.0+-x64-linux.tar.gz
&&
\
tar
zxvpf ncbi-blast-2.10.0+-x64-linux.tar.gz
&&
\
tar
zxvpf ncbi-blast-2.10.0+-x64-linux.tar.gz
&&
\
cp
/tmp/ncbi-blast-2.10.0+/bin/makeblastdb /usr/local/bin/
&&
\
cp
/tmp/ncbi-blast-2.10.0+/bin/makeblastdb /usr/local/bin/
&&
\
cp
/tmp/ncbi-blast-2.10.0+/bin/blastp /usr/local/bin/
&&
\
rm
ncbi-blast-2.10.0+-x64-linux.tar.gz
rm
ncbi-blast-2.10.0+-x64-linux.tar.gz
...
@@ -83,6 +84,7 @@ RUN wget http://www.microbesonline.org/fasttree/FastTree.c &&\
...
@@ -83,6 +84,7 @@ RUN wget http://www.microbesonline.org/fasttree/FastTree.c &&\
gcc
-DOPENMP
-fopenmp
-DUSE_DOUBLE
-Wall
-O3
-finline-functions
-funroll-loops
-o
FastTreeMP FastTree.c
-lm
&&
\
gcc
-DOPENMP
-fopenmp
-DUSE_DOUBLE
-Wall
-O3
-finline-functions
-funroll-loops
-o
FastTreeMP FastTree.c
-lm
&&
\
ln
-s
/tmp/FastTreeMP /usr/local/bin
ln
-s
/tmp/FastTreeMP /usr/local/bin
## Install FastME FastME 2.1.6.1
## Install FastME FastME 2.1.6.1
WORKDIR
/tmp
WORKDIR
/tmp
RUN
apt-get
install
-y
automake
&&
\
RUN
apt-get
install
-y
automake
&&
\
...
...
This diff is collapsed.
Click to expand it.
Preview
0%
Loading
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment