Merge main into dev #224
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Merge main into dev #224
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…ts in the pipeline directory
resolved #27 removed the 2.7 from the shebang of all the python scripts in the pipeline directory.
Made clear that this version of Autometa uses Python 2.7.
…lting in always downloading nr.gz.Fixed file path handling to be less arch specific and updated variables for readability. (#35)
…meta databases directory (#37)
- update git clone location - 🎨💚 Correct repo URL in Dockerfile - 📝 Correct repo URL in LCA_README.md and README.md Co-authored-by: Jason Kwan <jkwan@pharmacy.wisc.edu>
Add support request template
Add help wanted label as default for support request
* Fix GitHub path to Autometa * 🎨 Change MAINTAINER (deprecated) to LABEL
…tly using `--update` flag) (#116) 🎨 Add python 3 compatibility for urllib and print statements. 🎨 change update_databases(...) to prepare_databases(...) and add arg for explicitly updating 🎨 Applied black formatting.
🐛 Fix "completness" typo in cluster_process.py
…bal install with read-only access to marker folder (#139)
* 🎨 Apply formatting on pipeline and validation directories with 2to3 🎨 Apply black formatting on 2to3 output 🔥 Remove unused imports in recursive_dbscan.py ⬆️ Add requirements.txt for easier installation using conda create -n autometa -c conda-forge -c bioconda --file=requirements.txt * 🎨 Apply formatting on pipeline and validation directories with 2to3 🎨 Apply black formatting on 2to3 output 🔥 Remove unused imports in recursive_dbscan.py * 🐳 Update Dockerfile for py3 installation 🔥 Remove unused imports in ML_recruitment.py * 🎨 Add EOF line to Dockerfile * 🔥 Remove unused import from run_autometa.py 🐳🎨 hmmpress markers databases * 📝 Update installation instructions * Reverse compatibility note for py2.7 and py3 * 🎨📝 Reformatting headers in installation * 🔥 Remove typo * 🎨🐛 Allow for gzipped prot.accession2taxid when checking databases * 🐛 Chain decode to subprocess.check_output(...) when checking downloaded md5 * 🎨 Add text=True param to subprocess.check_output(...) calls 🎨 run 2to3 and black on lca_functions.pyx * 🎨 Add subprocess.check_output(..., text=True) to validation dir scripts * 🐛 Add `db_dir_path` param to run_blast2lca(...) in make_taxonomy_table.py * 🐳 Add pipeline and validation dirs to /Users/rees/miniconda3/bin:/Users/rees/miniconda3/condabin:/usr/local/opt/mysql-client/bin:/Users/rees/bin:/usr/local/bin:/usr/local/Cellar/pyenv-virtualenv/HEAD-5419dc7/shims:/Users/rees/.pyenv/shims:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/usr/local/go/bin:/Applications/Postgres.app/Contents/Versions/latest/bin * 🐳🎨 Add EOF char to Dockerfile * 🐳🔥 Remove apt-get comment 🐳📝 Update copyright to 2021 info * 🐛 Add encoding instance check and convert bytes objects to str in init_logger(...) * 🎨🐛🔥 Change length_trim(...) func to handle gzipped fastas using SeqIO rather than perl script 🔥 Deprecated fasta_length_trim.pl from run_autometa.py * 🔥 Remove logger emit message (logging is not imported in run_autometa_docker.py) * 🎨 black formatting * Update README.md Co-authored-by: Jason Kwan <jason.kwan@wisc.edu> * :art add /output/ prefix to coverage table output in make_taxonomy_table_docker.py 🎨 reformat some commands with f-strings * 🎨 change shebangs from python2.7 to python 🎨 add database check if taxonomy table is specified in run_autometa_docker * :memo Add note on python versions in README 📝🐛 move change directory command above hmmpress in environment build example in README * 🐛🐳 Fix apt-get update error during docker build Error message: InRelease' changed its 'Suite' value from 'stable-updates' to 'oldstable-updates' Suggested fix was found here: https://vitux.com/fixed-n-repository-http-security-debian-org-buster-updates-inrelease-changed-its-version-value-from-to-10/ - 📝 Add docker build command to readme - 📝 Add 🐳 to git commit style messages in CONTRIBUTING * 🎨 Add implementation to handle gzipped assemblies in make_taxonomy_table.py * 🎨🐛 Fix path incorrect file path handling when gzipped assembly is provided to length_filter(...) causing diamond blastp to use wrong filepath as query * 🎨🐛 Fix incorrect path handling where .filtered.orfs gets appended twice and is passed in wrong to run_diamond * 🎨 Reformatting some print statements with f-strings for ease of reading * 🔥🐛 Remove hardcoded extension in orfs_fpath param for run_diamond(...) func in make_taxonomy_table.py * 📝 Update readme to fix markdown-lint warnings and add `--db_dir` parameter to example usage * 📝 replace databases path to new GH repo name NOTE: This assumes Autometa was installed in the user\'s home directory * 📝 Replace any filepath instance of autometa with Autometa and \~ with $HOME * Update pipeline/make_taxonomy_table.py Co-authored-by: Jason Kwan <jason.kwan@wisc.edu>
Fix typo where url and description to miniconda were not hyperlinked
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