| name: socialgene_nf | |
| channels: | |
| - conda-forge | |
| - bioconda | |
| - defaults | |
| dependencies: | |
| - conda-forge::python>=3.10 | |
| - bioconda::hmmer>=3.3.2 |
| include common_parameters.env | |
| export | |
| SHELL = /bin/bash | |
| CURRENT_UID := $(shell id -u) | |
| CURRENT_GID := $(shell id -g) | |
| export CURRENT_UID | |
| export CURRENT_GID |
| Sep-01 20:50:45.862 [main] DEBUG nextflow.cli.Launcher - $> nextflow run . -profile ultraquickstart,conda --single_outdir /home/chase/Documents/ultraqsauickstart/test -resume | |
| Sep-01 20:50:45.917 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 22.04.0 | |
| Sep-01 20:50:46.711 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /home/chase/Documents/github/kwan_lab/socialgene/sgnf/nextflow.config | |
| Sep-01 20:50:46.712 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/chase/Documents/github/kwan_lab/socialgene/sgnf/nextflow.config | |
| Sep-01 20:50:46.718 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `ultraquickstart,conda` | |
| Sep-01 20:50:46.942 [main] DEBUG nextflow.plugin.PluginsFacade - Using Default plugins manager | |
| Sep-01 20:50:46.949 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] | |
| Sep-01 20:50:46.949 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] | |
| Sep-01 20:50:46.951 [main] INFO org.pf4j.DefaultPlug |
| import requests | |
| from pathlib import Path | |
| def dl_subsequence_gbk(outdir, accession, n_start, n_stop): | |
| response = requests.post( | |
| "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi", | |
| params={ | |
| "db": "nuccore", | |
| "rettype": "gb", | |
| "from": str(n_start), |
| # template.sub | |
| # starter submit file for CHTC jobs | |
| universe = vanilla | |
| log = logs/job_$(Cluster).log | |
| error = errors/job_$(Cluster)_$(Process).err | |
| output = outputs/job_$(Cluster)_$(Process).out | |
| executable = hmmsearch.sh | |
| arguments = $(hmm_model_basename) $(fasta_file_basename) |
| /* | |
| ======================================================================================== | |
| Nextflow minimal test | |
| ======================================================================================== | |
| Defines input files and everything required to run a fast and simple pipeline test. | |
| Use as follows: | |
| outdir='/home/chase/Documents/socialgene_data/buchnera' |
| import zstandard as zstd | |
| def decompress_zstd(bytes_input): | |
| dctx = zstd.ZstdDecompressor() | |
| decompressed_domtblout = dctx.decompress(bytes_input) | |
| return decompressed_domtblout.decode("utf-8").splitlines() | |
| cctx = zstandard.ZstdCompressor() | |
| compressed = cctx.compress(b"data to compress") |
| FROM mambaorg/micromamba:0.23.3 | |
| COPY --chown=$MAMBA_USER:$MAMBA_USER antismash.yml /tmp/env.yaml | |
| RUN micromamba create -n antismash | |
| RUN micromamba install --yes --file /tmp/env.yaml && \ | |
| micromamba clean --all --yes | |
| ARG MAMBA_DOCKERFILE_ACTIVATE=1 | |
| ENV ENV_NAME=antismash |
Download and install RStudio
Download and install R (follow the link for your type of comput, under "Download and Install R")
We're probably not going to do much actual work within IDBac, but installing IDBac will also install some other dependencies we will use.
Open RStudio and run the following commands:
| Create directory ./tmp | |
| easy-cluster pass.fasta mmseqs2_pass ./tmp --threads 24 | |
| MMseqs Version: 13.45111 | |
| Substitution matrix nucl:nucleotide.out,aa:blosum62.out | |
| Seed substitution matrix nucl:nucleotide.out,aa:VTML80.out | |
| Sensitivity 4 | |
| k-mer length 0 | |
| k-score 2147483647 | |
| Alphabet size nucl:5,aa:21 |