PhyloSkims/annotate
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Changes to be committed:

Browse Source 
modified:   .gitignore
	new file:   data/cds/sp_chlorodb/parameters.sh
	deleted:    data/ir/LSC_RefDB.fasta
	deleted:    data/ir/SSC_RefDB.fasta
	modified:   detectors/cds/bin/go_cds.sh
	modified:   detectors/normalize/lib/lookforIR.lib.sh
	modified:   detectors/normalize/lib/selectIR.py
	modified:   organnot/Dockerfile
	new file:   organnot/README.md
	new file:   organnot/dorgannot
	deleted:    ports/.DS_Store
	deleted:    src/ncbiblast/binaries/.gitignore
	deleted:    src/prokov/lxpack/tests/S.fasta
	deleted:    src/prokov/lxpack/tests/St.fasta
	deleted:    src/prokov/lxpack/tests/Stt.fasta
	deleted:    src/prokov/lxpack/tests/aS.fasta
	deleted:    src/prokov/lxpack/tests/aSt.fasta
	deleted:    src/prokov/lxpack/tests/aStt.fasta
	deleted:    src/prokov/lxpack/tests/aaS.fasta
	deleted:    src/prokov/lxpack/tests/aaSt.fasta
	deleted:    src/prokov/lxpack/tests/aaStt.fasta
	new file:   src/repseek/repseek-2014.09.tgz
This commit is contained in:
Eric Coissac
2025-03-05 21:56:39 +01:00
parent 5d09615f27
commit 4b71fe8c4c
22 changed files with 94 additions and 75646 deletions
Download Patch File Download Diff File Expand all files Collapse all files

34
organnot/Dockerfile
View File

@ -1,4 +1,4 @@
FROM ubuntu:lunar as builder
FROM ubuntu:jammy AS builder
LABEL dockerfile.version="1"
LABEL software="phyloskims"
@ -9,10 +9,10 @@ LABEL software="phyloskims"
##
WORKDIR /
RUN apt update --fix-missing && apt upgrade -y
RUN apt install -y build-essential
RUN apt install -y git tcsh bash gawk parallel gettext zlib1g-dev libglib2.0-0
RUN git clone https://git.metabarcoding.org/org-asm/org-annotate.git
RUN apt-get update --fix-missing && apt upgrade -y
RUN apt-get install -y build-essential
RUN apt-get install -y git tcsh bash gawk parallel gettext zlib1g-dev libglib2.0-0
RUN git clone https://github.com/PhyloSkims/annotate.git org-annotate
#
# Compile tools
@ -28,14 +28,14 @@ RUN make
#
##
WORKDIR "/"
RUN apt install -y python3-pip python3-dev python3-venv
RUN git clone https://git.metabarcoding.org/org-asm/org-asm.git
RUN python3 -m venv org-assembler
WORKDIR "/org-asm"
RUN bash -c '../org-assembler/bin/pip3 install -r requirements.txt'
RUN bash -c '../org-assembler/bin/python3 setup.py install --no-serenity'
WORKDIR "/"
# WORKDIR "/"
# RUN apt install -y python3-pip python3-dev python3-venv
# RUN git clone https://git.metabarcoding.org/org-asm/org-asm.git
# RUN python3 -m venv org-assembler
# WORKDIR "/org-asm"
# RUN bash -c '../org-assembler/bin/pip3 install -r requirements.txt'
# RUN bash -c '../org-assembler/bin/python3 setup.py install --no-serenity'
# WORKDIR "/"
##
#
@ -43,14 +43,14 @@ WORKDIR "/"
#
##
FROM ubuntu:lunar as phyloskims
FROM ubuntu:jammy AS phyloskims
WORKDIR /
RUN apt update --fix-missing && apt upgrade -y
RUN apt install -y tcsh bash gawk parallel zlib1g libglib2.0-0 clustalo muscle cd-hit hmmer
RUN apt-get install -y tcsh bash gawk parallel zlib1g libglib2.0-0 clustalo muscle cd-hit hmmer
COPY --from=builder /org-annotate /org-annotate
RUN rm -rf /org-annotate/src
COPY --from=builder /org-assembler /org-assembler
COPY --from=builder /org-assembler/bin/oa /bin
# COPY --from=builder /org-assembler /org-assembler
# COPY --from=builder /org-assembler/bin/oa /bin
COPY organnot /bin
RUN chmod +x /bin/organnot
#

5
organnot/README.md Normal file
View File

@ -0,0 +1,5 @@
To build the docker image:
```bash
docker build --load --platform linux/amd64 -t phyloskims/annotate .
```

15
organnot/dorgannot Executable file
View File

@ -0,0 +1,15 @@
#!/bin/bash
#IMAGE=gricad-registry.univ-grenoble-alpes.fr/leca/projets/malbio/phyloskims
IMAGE=phyloskims/annotate
TAG=latest
singularity -h >/dev/null 2>&1 && DOCKER="singularity --silent exec --bind .:/data docker://"
docker -h >/dev/null 2>&1 && DOCKER="docker run --volume .:/data "
if [[ -z "$DOCKER" ]] ; then
echo "Cannot found neither singularity or docker on your system"
exit 1
fi
eval "${DOCKER}${IMAGE}:${TAG} organnot $*"