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

Non root install #6

Open
wants to merge 47 commits into
base: ubuntu14.04/v1.1
Choose a base branch
from
Open

Non root install #6

Show file tree
Hide file tree
Changes from 45 commits
Commits
Show all changes
47 commits
Select commit Hold shift + click to select a range
2bb35a8
Added non root install instructions
themangoemoji Oct 28, 2014
cd21e3f
EC2 non root install instructions
themangoemoji Oct 31, 2014
becd6f3
pipeline notes and prokka install update
themangoemoji Oct 31, 2014
4a87f7f
pipline note update
themangoemoji Nov 4, 2014
5e8fbd9
changed ~ to /Users/narrows
themangoemoji Nov 4, 2014
dc86e93
rename
themangoemoji Nov 4, 2014
caaa0bb
no mo .profile
themangoemoji Nov 4, 2014
a966b79
no mo .profile
themangoemoji Nov 4, 2014
92bda18
Merge branch 'non-root-install' of github.com:ged-lab/2012-paper-digi…
themangoemoji Nov 4, 2014
3d15fcf
Add RackSpace install instructions
themangoemoji Jan 23, 2015
74bf7d9
Add RackSpace install instructions
themangoemoji Jan 23, 2015
b66eae0
Shake installs out of install-prokka script
themangoemoji Jan 27, 2015
31e9b73
Change install location to ~/src
themangoemoji Jan 30, 2015
9d08ddd
Check out the correct branch, curl correct file
themangoemoji Jan 30, 2015
bfce3b7
Check out the correct branch, curl correct file
themangoemoji Jan 30, 2015
c78f9ba
Merge branch 'non-root-install' of https://github.com/ged-lab/2012-pa…
themangoemoji Jan 30, 2015
55a61f3
Add rackspace instructions and prokka install updates
themangoemoji Feb 10, 2015
4b29611
Merge branch 'non-root-install' of github.com:ged-lab/2012-paper-digi…
themangoemoji Feb 10, 2015
2568739
Upgrade numpy
themangoemoji Feb 10, 2015
fcaf3d0
Seperate EC2 and RackSpace instructions
themangoemoji Feb 17, 2015
353bacb
Expand arguments for Makefile commands
themangoemoji Feb 17, 2015
88e9fa3
Add additional targets for missing files and download data
themangoemoji Feb 17, 2015
a3c77a4
Rerout /mnt/bin to ${HOME}/bin
themangoemoji Feb 18, 2015
6438276
Resolve merge
themangoemoji Feb 18, 2015
727aa85
Merge branch 'non-root-install' of https://github.com/ged-lab/2012-pa…
themangoemoji Feb 18, 2015
8d3b137
Rerout /mnt/bin to ${HOME}/bin
themangoemoji Feb 18, 2015
763a608
Update prokka-11 install
themangoemoji Feb 24, 2015
99eac72
Merge with athyra
themangoemoji Feb 24, 2015
c21b7ba
Merging athyra/local differences
themangoemoji Feb 24, 2015
e8e8a0a
Update notes with proper root/non-root distinctions
themangoemoji Feb 24, 2015
ff79fd1
Merge branch 'non-root-install' of github.com:ged-lab/2012-paper-digi…
themangoemoji Feb 24, 2015
b6fd3f0
Fix install-prokka script
themangoemoji Feb 24, 2015
28a9afe
Fix install-prokka script
themangoemoji Feb 24, 2015
83eade1
Merge branch 'non-root-install' of github.com:ged-lab/2012-paper-digi…
themangoemoji Feb 24, 2015
188a66f
Merge branch 'non-root-install' of github.com:ged-lab/2012-paper-digi…
themangoemoji Feb 24, 2015
e240d39
Merge branch 'non-root-install' of github.com:ged-lab/2012-paper-digi…
themangoemoji Feb 25, 2015
17d9f17
Fixup pipeline notes
themangoemoji Feb 25, 2015
29db18f
Move numpy install to root installs
themangoemoji Mar 17, 2015
a3328ba
Point root to install in user directory
themangoemoji Mar 17, 2015
f525527
Switch home to usert
themangoemoji Mar 17, 2015
1bf737d
Add prodigal to root installs, change path variable ordering
themangoemoji Apr 21, 2015
51e8670
Allow non-root to own their directory
themangoemoji Apr 21, 2015
83267f2
Add screed install
themangoemoji Apr 21, 2015
a890134
Move screed install to non-root
themangoemoji Apr 28, 2015
90cfefd
Correct thread variable syntax
themangoemoji Apr 28, 2015
081d1e7
Use `prokka` directly in makefile, Update pipeline-notes
themangoemoji May 3, 2015
d5dcf9e
Fix user-land installs to use sudo
themangoemoji May 21, 2015
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
3 changes: 0 additions & 3 deletions .profile
View file
Open in desktop

This file was deleted.

18 changes: 18 additions & 0 deletions pipeline/.gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -133,3 +133,21 @@ sar_assembly.report
sar_assembly.snps
sar_assembly.unqry
sar_assembly.unref
../pipeline-data-new.tar.gz
bacteria_mda_lane1.fastq.bz2.normC20k20.ct
bacteria_mda_lane7.fastq.bz2.normC20k20.ct
ecoli_ref-5m.fastq.ct
ecoli_ref-5m.fastq.ct.info
ecoli_ref.fastq.bz2.normC20k20.ct
genome-reads.fa.ct
genome-reads.fa.ct.info
genome-reads.fa.keep.abundfilt.keep.ct
genome-reads.fa.keep.ct
mouse-5m.fq.ct
mouse-5m.fq.ct.info
random.fa.pt
transcript-reads.fa.ct
transcript-reads.fa.ct.info
transcript-reads.fa.keep.abundfilt.keep.ct
transcript-reads.fa.keep.ct
transcripts.fa.pt
63 changes: 36 additions & 27 deletions pipeline/Makefile
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,6 @@
#default to setting number of threads to number of processors
THREADS != $(shell nproc)

all: genome-reads.fa.ct genome-reads.fa.keep \
random.x.genome-reads.fa.overlap \
random.x.genome-reads.fa.keep.overlap \
Expand Down Expand Up @@ -88,7 +91,7 @@ genome-reads.fa.keep: genome-reads.fa
genome-reads.fa.keep.abundfilt: genome-reads.fa.keep
filter-abund.py genome-reads.fa.keep.ct genome-reads.fa.keep

genome-reads.fa.keep.abundfilt.keep: genome-reads.fa.keep.abundfilt
genome-reads.fa.keep.abundfilt.keep genome-reads.fa.keep.abundfilt.keep.ct: genome-reads.fa.keep.abundfilt
normalize-by-median.py -k 20 -N 4 -x 1e8 -C 5 --savetable genome-reads.fa.keep.abundfilt.keep.ct genome-reads.fa.keep.abundfilt

random.x.genome-reads.fa.overlap: genome-reads.fa
Expand Down Expand Up @@ -116,7 +119,7 @@ transcript-reads.fa.keep: transcript-reads.fa
transcript-reads.fa.keep.abundfilt: transcript-reads.fa.keep
filter-abund.py transcript-reads.fa.keep.ct transcript-reads.fa.keep

transcript-reads.fa.keep.abundfilt.keep: transcript-reads.fa.keep.abundfilt
transcript-reads.fa.keep.abundfilt.keep transcript-reads.fa.keep.abundfilt.keep.ct: transcript-reads.fa.keep.abundfilt
normalize-by-median.py -k 20 -N 4 -x 1e8 -C 5 --savetable transcript-reads.fa.keep.abundfilt.keep.ct transcript-reads.fa.keep.abundfilt

transcript-reads.fa.keep.abundfilt.keep: transcript-reads.fa.keep.abundfilt
Expand Down Expand Up @@ -148,16 +151,16 @@ samfoo:
samtools faidx transcripts.fa

genome-reads.fa.map: random.1.ebwt
bowtie -f -a --best --strata random genome-reads.fa > genome-reads.fa.map
bowtie -f --all --best --strata random genome-reads.fa > genome-reads.fa.map

genome-reads.fa.sam:
bowtie -S -f random genome-reads.fa > genome-reads.fa.sam
bowtie --sam -f random genome-reads.fa > genome-reads.fa.sam

transcript-reads.fa.sam:
bowtie -S -f transcripts transcript-reads.fa > transcript-reads.fa.sam
bowtie --sam -f transcripts transcript-reads.fa > transcript-reads.fa.sam

transcript-reads.fa.map: transcripts.1.ebwt
bowtie -f -a --best --strata transcripts transcript-reads.fa > transcript-reads.fa.map
bowtie -f --all --best --strata transcripts transcript-reads.fa > transcript-reads.fa.map

genome-reads.fa.bam: genome-reads.fa.sam
samtools view -bt random.fa.fai genome-reads.fa.sam > genome-reads.fa.bam
Expand All @@ -170,10 +173,10 @@ genome-reads.fa.counts.pickle: genome-reads.fa.map
python mapping-cov-3.py random.fa genome-reads.fa.map genome-reads.fa.counts.pickle

genome-reads.fa.keep.map: random.1.ebwt
bowtie -f -a --best --strata random genome-reads.fa.keep > genome-reads.fa.keep.map
bowtie -f --all --best --strata random genome-reads.fa.keep > genome-reads.fa.keep.map

genome-reads.fa.keep.abundfilt.keep.map:
bowtie -f -a --best --strata random genome-reads.fa.keep.abundfilt.keep > genome-reads.fa.keep.abundfilt.keep.map
bowtie -f --all --best --strata random genome-reads.fa.keep.abundfilt.keep > genome-reads.fa.keep.abundfilt.keep.map

genome-reads.fa.map.cov: genome-reads.fa.map
python mapping-genome-cov-3.py random.fa genome-reads.fa.map genome-reads.fa.map.cov
Expand All @@ -188,13 +191,13 @@ ecoli_ref-5m.fastq.ct: ecoli_ref-5m.fastq
load-into-counting.py -k 20 -N 4 -x 5e8 ecoli_ref-5m.fastq.ct ecoli_ref-5m.fastq

ecoli_ref-5m.fastq.map: ecoli_ref-5m.fastq ecoliMG1655.1.ebwt
bowtie -q -a --best --strata ecoliMG1655 ecoli_ref-5m.fastq > ecoli_ref-5m.fastq.map
bowtie -q --all --best --strata ecoliMG1655 ecoli_ref-5m.fastq > ecoli_ref-5m.fastq.map

ecoli_ref-5m.fastq.map.cov: ecoli_ref-5m.fastq.map
python mapping-genome-cov-3.py ecoliMG1655.fa ecoli_ref-5m.fastq.map ecoli_ref-5m.fastq.map.cov

ecoli_ref-5m.fastq.sam:
bowtie -S -q -a --best --strata ecoliMG1655 ecoli_ref-5m.fastq > ecoli_ref-5m.fastq.sam
bowtie -S -q --all --best --strata ecoliMG1655 ecoli_ref-5m.fastq > ecoli_ref-5m.fastq.sam

ecoli_ref-5m.fastq.bam: ecoli_ref-5m.fastq.sam
samtools view -bt random.fa.fai ecoli_ref-5m.fastq.sam > ecoli_ref-5m.fastq.bam
Expand All @@ -207,13 +210,13 @@ ecoli_ref-5m.fastq.sorted.bam: ecoli_ref-5m.fastq.bam


ecoli_ref.fastq.bz2.keep.map: ecoli_ref.fastq.bz2.keep
bowtie -q -a --best --strata ecoliMG1655 ecoli_ref.fastq.bz2.keep > ecoli_ref.fastq.bz2.keep.map
bowtie -q --all --best --strata ecoliMG1655 ecoli_ref.fastq.bz2.keep > ecoli_ref.fastq.bz2.keep.map

ecoli_ref.fastq.bz2.keep.map.cov: ecoli_ref.fastq.bz2.keep.map
python mapping-genome-cov-3.py ecoliMG1655.fa ecoli_ref.fastq.bz2.keep.map ecoli_ref.fastq.bz2.keep.map.cov

genome-reads.fa.keep.sam:
bowtie -S -f random genome-reads.fa.keep > genome-reads.fa.keep.sam
bowtie --sam -f random genome-reads.fa.keep > genome-reads.fa.keep.sam

genome-reads.fa.keep.bam: genome-reads.fa.keep.sam
samtools view -bt random.fa.fai genome-reads.fa.keep.sam > genome-reads.fa.keep.bam
Expand Down Expand Up @@ -260,7 +263,7 @@ trinity-300.1.ebwt: trinity-300.fa
bowtie-build trinity-300.fa trinity-300

mouse-5m.fq.map: mouse-5m.fq trinity-300.1.ebwt
bowtie -q -a --best --strata trinity-300 mouse-5m.fq > mouse-5m.fq.map
bowtie -q --all --best --strata trinity-300 mouse-5m.fq > mouse-5m.fq.map

mouse-5m.fq.ct: mouse-5m.fq
load-into-counting.py -k 20 -N 4 -x 1e9 mouse-5m.fq.ct mouse-5m.fq
Expand All @@ -287,13 +290,13 @@ mouse-5m.fq.keep: mouse-5m.fq
normalize-by-median.py -k 20 -N 4 -x 1e9 mouse-5m.fq

mouse-5m.fq.keep.map: mouse-5m.fq.keep
bowtie -q -a --best --strata trinity-300 mouse-5m.fq.keep > mouse-5m.fq.keep.map
bowtie -q --all --best --strata trinity-300 mouse-5m.fq.keep > mouse-5m.fq.keep.map

mouse-5m.fq.keep.map.cov: mouse-5m.fq.keep.map
python mapping-genome-cov-3.py trinity-300.fa mouse-5m.fq.keep.map mouse-5m.fq.keep.map.cov

transcript-reads.fa.keep.map:
bowtie -f -a --best --strata transcripts transcript-reads.fa.keep > transcript-reads.fa.keep.map
bowtie -f --all --best --strata transcripts transcript-reads.fa.keep > transcript-reads.fa.keep.map

transcript-reads.fa.keep.map.cov: transcript-reads.fa.keep.map
python mapping-genome-cov-3.py transcripts.fa transcript-reads.fa.keep.map transcript-reads.fa.keep.map.cov
Expand Down Expand Up @@ -350,27 +353,27 @@ ecoli_ref.fastq.bz2.keep.assembly.fa: ecoli_ref.fastq.bz2.keep.abundfilt.keep
# cp ecoli.37/contigs.fa ecoli_ref.fastq.bz2.keep.assembly.fa

orig_vs_ecoli_assembly.report: ecoliMG1655.fa ecoli_ref.fastq.bz2.keep.assembly.fa
dnadiff ecoliMG1655.fa ecoli_ref.fastq.bz2.keep.assembly.fa -p orig_vs_ecoli_assembly
dnadiff ecoliMG1655.fa ecoli_ref.fastq.bz2.keep.assembly.fa -prefix orig_vs_ecoli_assembly

ecoli_dn.faa: ecoli_ref.fastq.bz2.keep.assembly.fa
/mnt/prokka-1.7/bin/prokka ecoli_ref.fastq.bz2.keep.assembly.fa --outdir ecoli_dn --prefix ecoli_dn --force
${HOME}/src/prokka/prokka-* ecoli_ref.fastq.bz2.keep.assembly.fa --outdir ecoli_dn --prefix ecoli_dn --force
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@mr-c
Here where I changed the prokka directories. I thought we talked about installing to ${HOME}/src/prokka/prokka-*/bin, but both that and ${HOME}/src/prokka/prokka-* throw the error below. Isn't this bin (next to the binaries) where we want these installs though? I don't think anywhere else is appropriate.

/home/wrightm/src/prokka/prokka-* sar.keep.assembly.fa --outdir sar_dn --prefix sar_dn --force
/bin/sh: /home/wrightm/src/prokka/prokka-1.11: Is a directory
make: *** [sar_dn.faa] Error 126

Copy link
Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

How about using the path ${HOME}/src/prokka/prokka-*/bin/prokka to match what was there before?

Copy link
Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

And according to https://github.com/ged-lab/2012-paper-diginorm/pull/6/files#diff-ba53c673353e6a7edb32d8c3bd0f6817R9 you shouldn't even have to use a full path, just call prokka

cp ecoli_dn/ecoli_dn.faa .

sar_dn.faa: sar.keep.assembly.fa
/mnt/prokka-1.7/bin/prokka sar.keep.assembly.fa --outdir sar_dn --prefix sar_dn --force
${HOME}/src/prokka/prokka-* sar.keep.assembly.fa --outdir sar_dn --prefix sar_dn --force
cp sar_dn/sar_dn.faa .

staph_dn.faa: staph.keep.assembly.fa
/mnt/prokka-1.7/bin/prokka staph.keep.assembly.fa --outdir staph_dn --prefix staph_dn --force
${HOME}/src/prokka/prokka-* staph.keep.assembly.fa --outdir staph_dn --prefix staph_dn --force
cp staph_dn/staph_dn.faa .

sar_orig.faa: sar324_contigs_lane1.fa
/mnt/prokka-1.7/bin/prokka sar324_contigs_lane1.fa --outdir sar_orig --prefix sar_orig --force
${HOME}/src/prokka/prokka-* sar324_contigs_lane1.fa --outdir sar_orig --prefix sar_orig --force
cp sar_orig/sar_orig.faa .

sar_orig.x.sar_dn: sar_orig.faa sar_dn.faa
formatdb -i sar_dn.faa -o T -p T
blastp -db sar_dn.fa -query sar_orig.faa -evalue 1e-3 -num_threads 4 \
blastp -db sar_dn.faa -query sar_orig.faa -evalue 1e-3 -num_threads 4 \
-num_descriptions 2 -num_alignments 2 -out sar_orig.x.sar_dn \
-seg yes

Expand All @@ -389,22 +392,22 @@ staph.1.ebwt: staph-genome.fa
bowtie-build staph-genome.fa staph

staph.rawreads.map.gz: staph.1.ebwt bacteria_mda_lane7.fastq.bz2
bunzip2 -c bacteria_mda_lane7.fastq.bz2 | bowtie -p 8 -q -a --best --strata staph - | gzip -9c > staph.rawreads.map.gz
bunzip2 -c bacteria_mda_lane7.fastq.bz2 | bowtie --threads ${THREADS} -q --all --best --strata staph - | gzip -9c > staph.rawreads.map.gz

ecoli.rawreads.map.gz: ecoliMG1655.1.ebwt ecoli_ref.fastq.bz2
bunzip2 -c ecoli_ref.fastq.bz2 | bowtie -p 8 -q -a --best --strata ecoliMG1655 - | gzip -9c > ecoli.rawreads.map.gz
bunzip2 -c ecoli_ref.fastq.bz2 | bowtie --threads ${THREADS} -q --all --best --strata ecoliMG1655 - | gzip -9c > ecoli.rawreads.map.gz

sar324.rawreads.map.gz: sar324.1.ebwt bacteria_mda_lane1.fastq.bz2
bunzip2 -c bacteria_mda_lane1.fastq.bz2 | bowtie -p 8 -q -a --best --strata sar324 - | gzip -9c > sar324.rawreads.map.gz
bunzip2 -c bacteria_mda_lane1.fastq.bz2 | bowtie --threads ${THREADS} -q --all --best --strata sar324 - | gzip -9c > sar324.rawreads.map.gz

staph.keep.rawreads.map.gz: staph.1.ebwt bacteria_mda_lane7.fastq.bz2.keep
cat bacteria_mda_lane7.fastq.bz2.keep | bowtie -p 8 -q -a --best --strata staph - | gzip -9c > staph.keep.rawreads.map.gz
cat bacteria_mda_lane7.fastq.bz2.keep | bowtie --threads ${THREADS} -q --all --best --strata staph - | gzip -9c > staph.keep.rawreads.map.gz

ecoli.keep.rawreads.map.gz: ecoliMG1655.1.ebwt ecoli_ref.fastq.bz2.keep
cat ecoli_ref.fastq.bz2.keep | bowtie -p 8 -q -a --best --strata ecoliMG1655 - | gzip -9c > ecoli.keep.rawreads.map.gz
cat ecoli_ref.fastq.bz2.keep | bowtie --threads ${THREADS} -q --all --best --strata ecoliMG1655 - | gzip -9c > ecoli.keep.rawreads.map.gz

sar324.keep.rawreads.map.gz: sar324.1.ebwt bacteria_mda_lane1.fastq.bz2.keep
cat bacteria_mda_lane1.fastq.bz2.keep | bowtie -p 8 -q -a --best --strata sar324 - | gzip -9c > sar324.keep.rawreads.map.gz
cat bacteria_mda_lane1.fastq.bz2.keep | bowtie --threads ${THREADS} -q --all --best --strata sar324 - | gzip -9c > sar324.keep.rawreads.map.gz

ecoli.keep.rawreads.map.gz.cov: ecoli.keep.rawreads.map.gz
python mapping-genome-cov-3.py ecoliMG1655.fa ecoli.keep.rawreads.map.gz ecoli.keep.rawreads.map.gz.cov
Expand All @@ -423,3 +426,9 @@ sar324.rawreads.map.gz.cov: sar324.rawreads.map.gz

staph.rawreads.map.gz.cov: staph.rawreads.map.gz
python mapping-genome-cov-3.py staph-genome.fa staph.rawreads.map.gz staph.rawreads.map.gz.cov

../pipeline-data-new.tar.gz:
cd ..; curl -O https://s3.amazonaws.com/public.ged.msu.edu/2012-paper-diginorm/pipeline-data-new.tar.gz

mapping.txt bacteria_mda_lane1.fastq.bz2 ecoliMG1655.fa trinity-300.fa sar324_contigs_lane1.fa staph-genome.fa mouse-5m.fq bacteria_mda_lane7.fastq.bz2 ecoli_ref-5m.fastq ecoli_ref.fastq.bz2: ../pipeline-data-new.tar.gz
cd ..; tar xzf pipeline-data-new.tar.gz
56 changes: 10 additions & 46 deletions pipeline/install-prokka.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,46 +1,10 @@
cd /mnt
curl -O http://www.vicbioinformatics.com/prokka-1.7.tar.gz
tar xzf prokka-1.7.tar.gz

cd /mnt
curl -O ftp://selab.janelia.org/pub/software/hmmer3/3.1b1/hmmer-3.1b1.tar.gz
tar xzf hmmer-3.1b1.tar.gz
cd hmmer-3.1b1/
./configure --prefix=/usr && make && make install

cd /mnt
curl -O http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn1.2.36.tgz
tar -xvzf aragorn1.2.36.tgz
cd aragorn1.2.36/
gcc -O3 -ffast-math -finline-functions -o aragorn aragorn1.2.36.c
cp aragorn /usr/local/bin

cd /mnt
curl -O http://prodigal.googlecode.com/files/prodigal.v2_60.tar.gz
tar xzf prodigal.v2_60.tar.gz
cd prodigal.v2_60/
make
cp prodigal /usr/local/bin

cd /mnt
curl -O ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz
gunzip linux64.tbl2asn.gz
mv linux64.tbl2asn tbl2asn
chmod +x tbl2asn
cp tbl2asn /usr/local/bin

cd /mnt
curl -O http://ftp.gnu.org/gnu/parallel/parallel-20130822.tar.bz2
tar xjvf parallel-20130822.tar.bz2
cd parallel-20130822/
ls
./configure && make && make install

cd /mnt
curl -O http://selab.janelia.org/software/infernal/infernal-1.1rc4.tar.gz
tar xzf infernal-1.1rc4.tar.gz
cd infernal-1.1rc4/
ls
./configure && make && make install


#!/bin/bash -ex

mkdir -p ${HOME}/src/prokka
cd ${HOME}/src/prokka
Copy link
Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

need to do a mkdir -p first here as well

curl -OL https://github.com/Victorian-Bioinformatics-Consortium/prokka/archive/v1.11.tar.gz
tar xzf v*.tar.gz
ln -s prokka-* prokka
echo "export PATH=${PATH}:${HOME}/src/prokka/prokka/bin" >> ~/.bashrc
export PATH=${PATH}:${HOME}/src/prokka/prokka/bin
prokka --setupdb
Loading