Skip to content

Commit 75a41c4

Browse files
erinyoungerinyoung
authored
Merge pull request #1492 from Kincekara/prokka
add prokka 1.15.6
2 parents 6f0f55c + e28e88f commit 75a41c4

File tree

3 files changed

+106
-1
lines changed

3 files changed

+106
-1
lines changed

‎README.md‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -276,7 +276,7 @@ To learn more about the docker pull rate limits and the open source software pro
276276
| [Porechop](https://hub.docker.com/r/staphb/porechop/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/porechop)](https://hub.docker.com/r/staphb/porechop) | <details><summary>Click to see all versions</summary> <ul><li>[0.2.4](./build-files/porechop/0.2.4/)</li></ul> </details> | https://github.com/rrwick/Porechop |
277277
| [PPanGGOLiN](https://hub.docker.com/r/staphb/ppanggolin/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ppanggolin)](https://hub.docker.com/r/staphb/ppanggolin) | <details><summary>Click to see all versions</summary> <ul><li>[1.2.105](./build-files/ppanggolin/1.2.105/)</li><li>[2.0.3](./build-files/ppanggolin/2.0.3/)</li><li>[2.0.5](./build-files/ppanggolin/2.0.5/)</li><li>[2.1.2](./build-files/ppanggolin/2.1.2/)</li><li>[2.2.1](./build-files/ppanggolin/2.2.1/)</li><li>[2.2.4](./build-files/ppanggolin/2.2.4/)</li><li>[2.2.5](./build-files/ppanggolin/2.2.5/)</li></ul> </details> | https://github.com/labgem/PPanGGOLiN |
278278
| [Primer3](https://hub.docker.com/r/staphb/primer3/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/primer3)](https://hub.docker.com/r/staphb/primer3) | <details><summary>Click to see all versions</summary> <ul><li>[2.3.4](./build-files/primer3/2.3.4/)</li><li>[2.6.1](./build-files/primer3/2.6.1/)</li></ul> </details> | https://github.com/primer3-org/primer3 |
279-
| [Prokka](https://hub.docker.com/r/staphb/prokka/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/prokka)](https://hub.docker.com/r/staphb/prokka) | <details><summary>Click to see all versions</summary> <ul><li>[1.13.4](./build-files/prokka/1.13/)</li><li>[1.14.0](./build-files/prokka/1.14.0/)</li><li>[1.14.5](./build-files/prokka/1.14.5/)</li><li>[1.14.6](./build-files/prokka/1.14.6/)</li></ul> </details> | https://github.com/tseemann/prokka |
279+
| [Prokka](https://hub.docker.com/r/staphb/prokka/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/prokka)](https://hub.docker.com/r/staphb/prokka) | <details><summary>Click to see all versions</summary> <ul><li>[1.13.4](./build-files/prokka/1.13/)</li><li>[1.14.0](./build-files/prokka/1.14.0/)</li><li>[1.14.5](./build-files/prokka/1.14.5/)</li><li>[1.14.6](./build-files/prokka/1.14.6/)</li><li>[1.15.6](./build-files/prokka/1.15.6/)</li></ul> </details> | https://github.com/tseemann/prokka |
280280
| [pyCirclize](https://hub.docker.com/r/staphb/pycirclize/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pycirclize)](https://hub.docker.com/r/staphb/pycirclize) | <details><summary>Click to see all versions</summary> <ul><li>[1.0.0](./build-files/pycirclize/1.0.0/)</li><li>[1.2.0](./build-files/pycirclize/1.2.0/)</li><li>[1.5.0](./build-files/pycirclize/1.5.0/)</li><li>[1.6.0](./build-files/pycirclize/1.6.0/)</li><li>[1.7.1](./build-files/pycirclize/1.7.1/)</li><li>[1.7.2](./build-files/pycirclize/1.7.2/)</li><li>[1.9.0](./build-files/pycirclize/1.9.0/)</li><li>[1.9.1](./build-files/pycirclize/1.9.1/)</li><li>[1.10.0](./build-files/pycirclize/1.10.0/)</li><li>[1.10.1](./build-files/pycirclize/1.10.1/)</li></ul> </details> | https://github.com/moshi4/pyCirclize |
281281
| [pyGenomeViz](https://hub.docker.com/r/staphb/pygenomeviz/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pygenomeviz)](https://hub.docker.com/r/staphb/pygenomeviz) | <details><summary>Click to see all versions</summary> <ul><li>[0.2.2](./build-files/pygenomeviz/0.2.2/)</li><li>[0.3.2](./build-files/pygenomeviz/0.3.2/)</li><li>[0.4.2](./build-files/pygenomeviz/0.4.2/)</li><li>[0.4.3](./build-files/pygenomeviz/0.4.3/)</li><li>[0.4.4](./build-files/pygenomeviz/0.4.4/)</li><li>[1.1.0](./build-files/pygenomeviz/1.1.0/)</li><li>[1.5.0](./build-files/pygenomeviz/1.5.0/)</li><li>[1.6.1](./build-files/pygenomeviz/1.6.1/)</li></ul> </details> | https://github.com/moshi4/pyGenomeViz |
282282
| [pyMLST](https://hub.docker.com/r/staphb/pymlst/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/pymlst)](https://hub.docker.com/r/staphb/pymlst) | <details><summary>Click to see all versions</summary> <ul><li>[2.1.5](./build-files/pymlst/2.1.5/)</li><li>[2.1.6](./build-files/pymlst/2.1.6/)</li><li>[2.2.2](./build-files/pymlst/2.2.2/)</li></ul> </details> | https://github.com/bvalot/pyMLST |

‎build-files/prokka/1.15.6/Dockerfile‎

Lines changed: 79 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,79 @@
1+
2+
ARG PROKKA_VER="1.15.6"
3+
ARG MINCED_VER="0.4.2"
4+
5+
FROM ubuntu:noble AS app
6+
7+
ARG PROKKA_VER
8+
ARG MINCED_VER
9+
10+
LABEL base.image="ubuntu:noble"
11+
LABEL dockerfile.version="1"
12+
LABEL software="Prokka"
13+
LABEL software.version="${PROKKA_VER}"
14+
LABEL description="Automated prokaryotic genome annotation tool"
15+
LABEL website="https://github.com/tseemann/prokka"
16+
LABEL license="https://github.com/tseemann/prokka#licence"
17+
LABEL maintainer="Curtis Kapsak"
18+
LABEL maintainer.email="kapsakcj@gmail.com"
19+
LABEL maintainer2="Kutluhan Incekara"
20+
LABEL maintainer2.email="kutluhan.incekara@ct.gov"
21+
22+
ARG DEBIAN_FRONTEND="noninteractive"
23+
24+
RUN apt-get update && apt-get install -y --no-install-recommends \
25+
wget \
26+
ca-certificates \
27+
perl \
28+
aragorn \
29+
barrnap \
30+
ncbi-blast+ \
31+
hmmer \
32+
infernal \
33+
parallel \
34+
bioperl \
35+
libbio-searchio-hmmer-perl \
36+
libxml-simple-perl \
37+
prodigal \
38+
ncbi-tools-bin \
39+
default-jre-headless \
40+
dpkg-dev \
41+
gcc &&\
42+
rm -rf /var/lib/apt/lists/* && apt-get autoclean
43+
44+
# ncbi-tools-bin provides table2asn
45+
# dpkg-dev and gcc is for suppressing a warning (may be removed)
46+
47+
# install minced
48+
RUN wget -q https://github.com/ctSkennerton/minced/releases/download/${MINCED_VER}/minced \
49+
https://github.com/ctSkennerton/minced/releases/download/${MINCED_VER}/minced.jar &&\
50+
chmod +x minced* &&\
51+
mv minced* /usr/local/bin/
52+
53+
# install prokka
54+
RUN wget -q https://github.com/tseemann/prokka/archive/refs/tags/v${PROKKA_VER}.tar.gz &&\
55+
tar -xvf v${PROKKA_VER}.tar.gz && rm v${PROKKA_VER}.tar.gz
56+
57+
ENV PATH=$PATH:/prokka-${PROKKA_VER}/bin \
58+
LC_ALL=C
59+
60+
# index database
61+
RUN prokka --setupdb
62+
63+
CMD ["prokka", "--help"]
64+
65+
WORKDIR /data
66+
67+
## Test ##
68+
FROM app AS test
69+
70+
ARG PROKKA_VER
71+
72+
RUN prokka --listdb &&\
73+
prokka --version &&\
74+
blastp -help &&\
75+
barrnap --help 2>&1 | grep Options &&\
76+
prodigal -h &&\
77+
tbl2asn --help
78+
79+
RUN prokka /prokka-${PROKKA_VER}/test/genome.fna

‎build-files/prokka/1.15.6/README.md‎

Lines changed: 26 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,26 @@
1+
# Prokka container
2+
3+
Main tool : [Prokka](https://github.com/tseemann/prokka)
4+
5+
Additional tools:
6+
7+
- prodigal 2.6.3
8+
- bedtools 2.31.1
9+
- barrnap 0.9
10+
- ncbi-blast+ 2.12.0
11+
- tbl2asn 25.3
12+
- hmmer 3.4
13+
- perl 5.38.2
14+
- bioperl 1.7.8
15+
- aragorn 1.2.41
16+
17+
Full documentation: [link to documentation](https://github.com/tseemann/prokka)
18+
19+
Automated prokaryotic genome annotation tool
20+
21+
## Example Usage
22+
23+
```bash
24+
# run prokka on the provided test FASTA file (plasmid sequence)
25+
prokka --cpus 2 --outdir asm --prefix asm test/plasmid.fna
26+
```

0 commit comments

Comments
 (0)