-
Notifications
You must be signed in to change notification settings - Fork 125
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
adding dnaapler version 0.8.1 (#1056)
Co-authored-by: Kutluhan Incekara <[email protected]>
- Loading branch information
Showing
3 changed files
with
95 additions
and
1 deletion.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,57 @@ | ||
| FROM mambaorg/micromamba:1.5.8 as app | ||
|
|
||
| USER root | ||
|
|
||
| WORKDIR / | ||
|
|
||
| ARG DNAAPLER_VER="0.8.1" | ||
|
|
||
| # metadata labels | ||
| LABEL base.image="mambaorg/micromamba:1.5.8" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="dnaapler" | ||
| LABEL software.version="${DNAAPLER_VER}" | ||
| LABEL description="Rotates chromosomes and more" | ||
| LABEL website="https://github.com/gbouras13/dnaapler" | ||
| LABEL license="MIT" | ||
| LABEL license.url="https://github.com/gbouras13/dnaapler/blob/main/LICENSE" | ||
| LABEL maintainer="Erin Young" | ||
| LABEL maintainer.email="[email protected]" | ||
|
|
||
| # install dependencies; cleanup apt garbage | ||
| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| wget \ | ||
| ca-certificates \ | ||
| procps && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
|
|
||
| # create the conda environment, install mykrobe via bioconda package; cleanup conda garbage | ||
| RUN micromamba create -n dnaapler -y -c bioconda -c defaults -c conda-forge dnaapler=${DNAAPLER_VER} && \ | ||
| micromamba clean -a -f -y | ||
|
|
||
| # set the PATH and LC_ALL for singularity compatibility | ||
| ENV PATH="/opt/conda/envs/dnaapler/bin/:${PATH}" \ | ||
| LC_ALL=C.UTF-8 | ||
|
|
||
| # set final working directory as /data | ||
| WORKDIR /data | ||
|
|
||
| # default command is to print help options | ||
| CMD [ "dnaapler", "--help" ] | ||
|
|
||
| # new base for testing | ||
| FROM app as test | ||
|
|
||
| # set working directory to /test | ||
| WORKDIR /test | ||
|
|
||
| # checking that tool is in PATH | ||
| RUN dnaapler --help && dnaapler --version | ||
|
|
||
| # downloads genome sequence and then extracts the last plasmid in the laziest way possible | ||
| RUN wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/025/259/185/GCA_025259185.1_ASM2525918v1/GCA_025259185.1_ASM2525918v1_genomic.fna.gz && \ | ||
| gunzip GCA_025259185.1_ASM2525918v1_genomic.fna.gz && \ | ||
| grep "CP104365.1" GCA_025259185.1_ASM2525918v1_genomic.fna -A 50000 > CP104365.1.fasta && \ | ||
| dnaapler mystery --prefix mystery_test --output mystery_test -i CP104365.1.fasta && \ | ||
| dnaapler plasmid --prefix plasmid_test --output plasmid_test -i CP104365.1.fasta && \ | ||
| ls mystery_test plasmid_test |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,37 @@ | ||
| # dnaapler container | ||
|
|
||
| Main tool : [dnappler](https://github.com/gbouras13/dnaapler) | ||
|
|
||
| Full documentation: [https://github.com/gbouras13/dnaapler](https://github.com/gbouras13/dnaapler) | ||
|
|
||
| > `dnaapler` is a simple python program that takes a single nucleotide input sequence (in FASTA format), finds the desired start gene using blastx against an amino acid sequence database, checks that the start codon of this gene is found, and if so, then reorients the chromosome to begin with this gene on the forward strand. | ||
| dnaapler has several commands for chromosomes, plasmids, and more. | ||
|
|
||
| ``` | ||
| Usage: dnaapler [OPTIONS] COMMAND [ARGS]... | ||
| Options: | ||
| -h, --help Show this message and exit. | ||
| -V, --version Show the version and exit. | ||
| Commands: | ||
| chromosome Reorients your sequence to begin with the dnaA chromosomal... | ||
| citation Print the citation(s) for this tool | ||
| custom Reorients your sequence with a custom database | ||
| mystery Reorients your sequence with a random gene | ||
| phage Reorients your sequence to begin with the terL large... | ||
| plasmid Reorients your sequence to begin with the repA replication... | ||
| ``` | ||
|
|
||
| WARNING: Does not support multifasta files. Each sequence must be processed individually. | ||
|
|
||
| ## Example Usage | ||
|
|
||
| ```bash | ||
| # for a fasta of a chromsome sequence | ||
| dnaapler chromosome --input chromosome.fasta --output dnaapler_chr | ||
|
|
||
| # for a fasta of a plasmid sequence | ||
| dnaapler plasmid --input plasmid.fasta --output dnaapler_plasmid | ||
| ``` |