adds SeqFu

[taylorpaisie]

Pull Request (PR) checklist:

• [ X] Include a description of what is in this pull request in this message.
• [ X] 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 )
• [ ]X 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)
  • (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
• [ X] Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
  • If this README is longer than 30 lines, there is an explanation as to why more detail was needed
• Dockerfile includes the recommended LABELS
• [ X] Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
• [ X] Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

[erinyoung]

I think file was included by accident

[erinyoung]

Do you know why the tests fail?

[taylorpaisie]

oh oops, i can take that out, just part of my debugging of the dockerfile, doesn't fail in the container now.

[erinyoung]

Do you think it's worthwhile to include the test files in the final image? It might be helpful to just have these copied into the test stage for testing if they aren't needed during run time.

[erinyoung]

This is looking great!

If you're looking for assistance with creating tests, seqtk uses some fastq files from this repository in its tests

I imagine for seqfu it'd be someting like

RUN wget -q https://github.com/StaPH-B/docker-builds/raw/master/tests/SARS-CoV-2/SRR13957123_1.fastq.gz && \
    wget -q https://github.com/StaPH-B/docker-builds/raw/master/tests/SARS-CoV-2/SRR13957123_2.fastq.gz && \
seqfu count -f SRR13957123_1.fastq.gz -r SRR13957123_2.fastq.gz

SeqFu also looks like it comes with its own tests and files which may be useful.

[taylorpaisie]

yes, so i originally had all the test files in the container but you mentioned it wasn't necessary, so maybe i'll just put in the seqfu test fastq files you suggested in the comment for the seqfu test in the dockerfile. Also thank you for your help and suggestions!!!

[erinyoung]

My apologies for my delayed response.

I think this looks great!

I did make some changes, though:

• I moved your labels to the 'app' stage (labels don't transfer between stages and they get lost)
• I added a CMD line to your 'app' stage (the CMD line is the default command that is run in a container, and we generally set that as the help message)
• I removed some tools from the apt-get layer of the 'app' stage.
• I added nim's version to the builder stage for "easy" updating later
• I added in the dev's mini.sh tests - which all seem to work except test-check.sh, so I've dropped it (To me, this looks like a dev thing and not an installation issue)

  Testing module: check 
------------------------------------------------------------ 
OK: Checked single end exit status (expected 0, got 0)
OK: Checked single end OK (expected 1, got 1)
OK: Checked single end libtype (expected SE, got SE)
OK: Checked single end sequence count (expected 7, got 7)
OK: Checked BAD single end exit status with --deep (expected 1, got 1)
OK: Counts checking BAD single end exit status with --deep (expected 0, got 1)
OK: Checked BAD paired end exit status with --deep (expected 2, got 2)
OK: Counts checking BAD paired end exit status with --deep (expected 0, got 0)
OK: Checked BAD single end exit status without --deep (expected 1, got 1)
OK: Counts checking BAD single end exit status without --deep (expected 0, got 1)
OK: Checked paired end (expected 1, got 1)
OK: Checked paired end exit status (expected 0, got 0)
OK: Checked paired end libtype (expected PE, got PE)
OK: Checked single end sequence count (2xSE) (expected 14, got 14)
OK: Checked INVALID paired end (expected 0, got 0)
OK: Checked INVALID paired end exit status (got 1)
OK: Checked INVALID paired end libtype (expected PE, got PE)
OK: Checked INVALID paired end sequence count (2xSE) (expected -, got -)
OK: Checked INVALID directory (/test/test/../data//primers) exit status (expected > 0, got 2)
FAIL: Checked INVALID directory line count (got 14 expected 13)
OK      SE      /test/data/primers/16S_flash.extendedFrags.fastq        4306    1989406 0
OK      SE      /test/data/primers/16S_flash.extendedFrags.fastq.gz     4306    1989406 0
OK      SE      /test/data/primers/16S_merge.fq.gz      6137    2596981 0
OK      SE      /test/data/primers/16S_vsearch_merge.fq.gz      3935    1818111 0
ERR     SE      /test/data/primers/artificial.fq.gz     -       -       2       Invalid character in sequence: < > in R2.REV+.middle;
OK      SE      /test/data/primers/its-merge.fq.gz      7299    1504898 0
OK      SE      /test/data/primers/se.fq.gz     234     70434   0
OK      SE      /test/data/primers/small.fq     4       360     0
OK      PE      /test/data/primers/16S_R1.fq.gz 12274   3694474 0
OK      PE      /test/data/primers/16Snano_R1.fq.gz     468     140868  0
ERR     PE      /test/data/primers/art_R1.fq.gz 7       -       4       R2=Invalid character in sequence: < > in R2.REV+.middle;First sequence names do not match (R1.startFOR+, R2.startREV+);Last sequence names do not match (R1.FOR1+.start-middle, );
OK      PE      /test/data/primers/its_R1.fq.gz 16000   3387804 0
OK      PE      /test/data/primers/itsfilt_R1.fq.gz     15618   3272396 0
OK      PE      /test/data/primers/pico_R1.fq.gz        24      7224    0
total 10M
-rw-rw-r-- 1 root root 869K Dec 19  2023 16S_R1.fq.gz
-rw-rw-r-- 1 root root 986K Dec 19  2023 16S_R2.fq.gz
-rw-rw-r-- 1 root root 4.1M Dec 19  2023 16S_flash.extendedFrags.fastq
-rw-rw-r-- 1 root root 606K Dec 19  2023 16S_flash.extendedFrags.fastq.gz
-rw-rw-r-- 1 root root  256 Dec 19  2023 16S_flash.hist
-rw-rw-r-- 1 root root 1.4K Dec 19  2023 16S_flash.histogram
-rw-rw-r-- 1 root root 1.1M Dec 19  2023 16S_merge.fq.gz
-rw-rw-r-- 1 root root 416K Dec 19  2023 16S_vsearch_merge.fq.gz
-rw-rw-r-- 1 root root  33K Dec 19  2023 16Snano_R1.fq.gz
-rw-rw-r-- 1 root root  38K Dec 19  2023 16Snano_R2.fq.gz
-rw-rw-r-- 1 root root  233 Dec 19  2023 art_R1.fq.gz
-rw-rw-r-- 1 root root  236 Dec 19  2023 art_R2.fq.gz
-rw-rw-r-- 1 root root  299 Dec 19  2023 artificial.fa.gz
-rw-rw-r-- 1 root root  333 Dec 19  2023 artificial.fq.gz
-rw-rw-r-- 1 root root 273K Dec 19  2023 its-merge.fq.gz
-rw-rw-r-- 1 root root 355K Dec 19  2023 its_R1.fq.gz
-rw-rw-r-- 1 root root 500K Dec 19  2023 its_R2.fq.gz
-rw-rw-r-- 1 root root 328K Dec 19  2023 itsfilt_R1.fq.gz
-rw-rw-r-- 1 root root 440K Dec 19  2023 itsfilt_R2.fq.gz
-rw-rw-r-- 1 root root 2.1K Dec 19  2023 pico_R1.fq.gz
-rw-rw-r-- 1 root root 2.3K Dec 19  2023 pico_R2.fq.gz
-rw-rw-r-- 1 root root  33K Dec 19  2023 se.fq.gz
-rw-rw-r-- 1 root root 1011 Dec 19  2023 small.fq
OK: Checked INVALID directory line error count (got 2 expected 2)
OK: Checked valid directory SEQFU_TMPDIR_nevlh5 exit status (expected 0, got 0)
OK: Checked valid directory line count SEQFU_TMPDIR_nevlh5/out (got 1 expected 1)
OK: Checked valid directory line error count (got 0 expected 0)
FAIL: Finished with 23 passed, 1 failed

[erinyoung]

@taylorpaisie , if you're okay with my changes, we can deploy this image to dockerhub and quay

[taylorpaisie]

@erinyoung looks good to me! Thanks for all your advice and help, it's really helping me get better and learn more about building docker containers!

[erinyoung]

Perfect!

I'm going to

1. merge this PR
2. deploy a 'seqfu' image to staphb's dockerhub and quay repositories
3. use both tags of '1.20.3' and 'latest'

[erinyoung]

Thank you for putting this together!

You can check the status of the deploy here : https://github.com/StaPH-B/docker-builds/actions/runs/11184872785