Update to TOSTADAS v4.0.0 (replaces tbl2asn with table2asn in conda environment.yml file)

[jessicarowell]

This update to TOSTADAS v4.0.0 only has one change. It removes tbl2asn from the environment.yml file and replaces it with table2asn. README (in this folder and in top-level repo) updated. No change to license.

Pull Request (PR) checklist:

• Include a description of what is in this pull request in this message.
• The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15 )
• Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number (i.e. spades/3.12.0/Dockerfile)
• Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
• Dockerfile includes the recommended LABELS
• Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
• Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

[erinyoung]

The tests worked:

#10 [test 1/1] RUN liftoff --version &&     samtools --version &&     python --version &&     table2asn -help
#10 0.349 v1.6.3
#10 0.384 samtools 1.15.1
#10 0.384 Using htslib 1.15.1
#10 0.384 Copyright (C) 2022 Genome Research Ltd.
#10 0.384 
#10 0.384 Samtools compilation details:
#10 0.384     Features:       build=configure curses=yes 
#10 0.384     CC:             /opt/conda/conda-bld/samtools_1649352267887/_build_env/bin/x86_64-conda-linux-gnu-cc
#10 0.384     CPPFLAGS:       -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/envs/tostadas/include
#10 0.384     CFLAGS:         -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/envs/tostadas/include -fdebug-prefix-map=/opt/conda/conda-bld/samtools_1649352267887/work=/usr/local/src/conda/samtools-1.15.1 -fdebug-prefix-map=/opt/conda/envs/tostadas=/usr/local/src/conda-prefix
#10 0.384     LDFLAGS:        -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/envs/tostadas/lib -Wl,-rpath-link,/opt/conda/envs/tostadas/lib -L/opt/conda/envs/tostadas/lib
#10 0.384     HTSDIR:         
#10 0.384     LIBS:           
#10 0.384     CURSES_LIB:     -ltinfow -lncursesw
#10 0.384 
#10 0.384 HTSlib compilation details:
#10 0.384     Features:       build=configure plugins=yes, plugin-path=/opt/conda/envs/tostadas/libexec/htslib libcurl=yes S3=yes GCS=yes libdeflate=yes lzma=yes bzip2=yes htscodecs=1.2.2
#10 0.384     CC:             /opt/conda/conda-bld/htslib_1649384579568/_build_env/bin/x86_64-conda-linux-gnu-cc
#10 0.384     CPPFLAGS:       -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/envs/tostadas/include
#10 0.384     CFLAGS:         -Wall -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/envs/tostadas/include -fdebug-prefix-map=/opt/conda/conda-bld/htslib_1649384579568/work=/usr/local/src/conda/htslib-1.15.1 -fdebug-prefix-map=/opt/conda/envs/tostadas=/usr/local/src/conda-prefix -fvisibility=hidden
#10 0.384     LDFLAGS:        -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/envs/tostadas/lib -Wl,-rpath-link,/opt/conda/envs/tostadas/lib -L/opt/conda/envs/tostadas/lib -fvisibility=hidden -rdynamic
#10 0.384 
#10 0.384 HTSlib URL scheme handlers present:
#10 0.384     built-in:	 preload, data, file
#10 0.384     Amazon S3:	 s3+https, s3+http, s3
#10 0.384     libcurl:	 imaps, pop3, gophers, http, smb, gopher, sftp, ftps, imap, smtp, smtps, rtsp, scp, ftp, telnet, mqtt, https, smbs, tftp, pop3s, dict
#10 0.384     S3 Multipart Upload:	 s3w, s3w+https, s3w+http
#10 0.391  -euk
#10 0.391    Assume eukaryote, and create missing mRNA features
#10 0.391  -suspect-rules <String>
#10 0.391    Path to a file containing suspect rules set. Overrides environment variable
#10 0.391    PRODUCT_RULES_LIST
#10 0.391  -allow-acc
#10 0.391    Allow accession recognition in sequence IDs. Default is local
#10 0.391  -intronless
#10 0.391    Intronless alignments
#10 0.391  -refine-prt-alignments
#10 0.391    Refine ProSplign aligments when processing .prt input
#10 0.391  -prt-alignment-filter-query <String>
#10 0.391    Filter query string for .prt alignments
#10 0.391  -logfile <File_Out>
#10 0.391    Error Log File
#10 0.391     * Incompatible with:  logxml
#10 0.391  -logxml <File_Out>
#10 0.391    XML Error Log File
#10 0.391     * Incompatible with:  logfile
#10 0.391  -split-logs
#10 0.391    Create unique log file for each output file
#10 0.391  -verbose
#10 0.391    Be verbose on reporting
#10 0.391  -huge
#10 0.391    Execute in huge-file mode
#10 0.391     * Incompatible with:  disable-huge
#10 0.391  -disable-huge
#10 0.391    Explicitly disable huge-files mode
#10 0.391     * Incompatible with:  huge
#10 0.391  -usemt <String>
#10 0.391    Try to use as many threads as:
#10 0.391          one
#10 0.391          two
#10 0.391          many
#10 0.391  -version
#10 0.391    Print version number;  ignore other arguments
#10 0.391  -version-full
#10 0.391    Print extended version data;  ignore other arguments
#10 0.391  -version-full-xml
#10 0.391    Print extended version data in XML format;  ignore other arguments
#10 0.391  -version-full-json
#10 0.391    Print extended version data in JSON format;  ignore other arguments
#10 0.391 
#10 0.391  *** Data source and object manager options
#10 0.391  -r
#10 0.391    Enable remote data retrieval
#10 0.391  -genbank
#10 0.391    Enable remote data retrieval using the Genbank data loader
#10 0.391  -gb-method <String>
#10 0.391    Semicolon-separated list of Genbank loader method(s)
#10 0.391     * Requires:  genbank
#10 0.391  -gb-snp <Boolean>
#10 0.391    Genbank SNP processor
#10 0.391     * Requires:  genbank
#10 0.391  -gb-wgs <Boolean>
#10 0.391    Genbank WGS processor
#10 0.391     * Requires:  genbank
#10 0.391  -gb-cdd <Boolean>
#10 0.391    Genbank SNP processor
#10 0.391     * Requires:  genbank
#10 0.391  -vdb
#10 0.391    Use VDB data loader.
#10 0.391     * Incompatible with:  novdb
#10 0.391  -novdb
#10 0.391    Do not use VDB data loader.
#10 0.391     * Incompatible with:  vdb
#10 0.391  -vdb-path <String>
#10 0.391    Root path for VDB look-up
#10 0.391  -sra
#10 0.391    Add the SRA data loader with no options.
#10 0.391     * Incompatible with:  sra-acc, sra-file
#10 0.391  -sra-acc <String>
#10 0.391    Add the SRA data loader, specifying an accession.
#10 0.391     * Incompatible with:  sra, sra-file
#10 0.391  -sra-file <String>
#10 0.391    Add the SRA data loader, specifying an sra file.
#10 0.391     * Incompatible with:  sra, sra-acc
#10 0.391 
#10 0.391  *** General application arguments
#10 0.391  -fetchall
#10 0.391    Search data in all available databases
#10 0.391  -conffile <File_In>
#10 0.391    Program's configuration (registry) data file
#10 0.391    Default = `table2asn.conf'
#10 0.391 
#10 DONE 0.4s

[erinyoung]

I added -f to the micromamba clean layer. Sometimes this makes the image slightly smaller.

[erinyoung]

Here's a link for the deploy: https://github.com/StaPH-B/docker-builds/actions/runs/11848551090

(Should finish soon)