adds integron finder - Githubissues

Kincekara commented 2 weeks ago

Closes #1071

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
[x] 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 commented 2 weeks ago

It looks like the tests worked:

#10 [test 2/2] RUN wget -q https://github.com/gem-pasteur/Integron_Finder/raw/master/tests/data/Replicons/NZ_CP016323.fna &&    integron_finder --local-max --circ --keep-tmp NZ_CP016323.fna &&    cat Results_Integron_Finder_NZ_CP016323/NZ_CP016323.summary &&    head Results_Integron_Finder_NZ_CP016323/NZ_CP016323.integrons
#10 1.424 
#10 1.424 **************************************************************************
#10 1.424  ___       _                               _____ _           _
#10 1.424 |_ _|_ __ | |_ ___  __ _ _ __ ___  _ __   |  ___(_)_ __   __| | ___ _ __
#10 1.424  | || '_ \| __/ _ \/ _` | '__/ _ \| '_ \  | |_  | | '_ \ / _` |/ _ \ '__|
#10 1.424  | || | | | ||  __/ (_| | | | (_) | | | | |  _| | | | | | (_| |  __/ |
#10 1.424 |___|_| |_|\__\___|\__, |_|  \___/|_| |_| |_|   |_|_| |_|\__,_|\___|_|
#10 1.424                    |___/
#10 1.424 
#10 1.424 **************************************************************************
#10 1.424 
#10 1.424 integron_finder version 2.0.5 
#10 1.424 Using:
#10 1.424  - Python 3.10.12 (main, Sep 11 2024, 15:47:36) [GCC 11.4.0]
#10 1.424  - numpy 2.1.1
#10 1.424  - pandas 2.2.3
#10 1.424  - matplolib 3.9.2
#10 1.424  - biopython 1.84
#10 1.424 
#10 1.424  - Prodigal V2.6.3: February, 2016
#10 1.424  - INFERNAL 1.1.4 (Dec 2020)
#10 1.424  - HMMER 3.3.2 (Nov 2020); http://hmmer.org/
#10 1.424 
#10 1.424 Authors:
#10 1.424  - Jean Cury, Bertrand Neron, Eduardo Rocha,
#10 1.424 
#10 1.424 Citation:
#10 1.424 
#10 1.424  Néron, B.; Littner, E.; Haudiquet, M.; Perrin, A.; Cury, J.; Rocha, E.P.C. 
#10 1.424  IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella. 
#10 1.424  Microorganisms 2022, 10, 700. https://doi.org/10.3390/microorganisms10040700
#10 1.424 
#10 1.424  If you use --func-annot in conjunction with file NCBIfam-AMRFinder.hmm please also cite
#10 1.424 
#10 1.424  Haft, DH et al., Nucleic Acids Res. 2018 Jan 4;46(D1):D851-D860
#10 1.424  PMID: 29112715
#10 1.424  
#10 1.424 
#10 1.424                      =======================
#10 1.424 
#10 1.424 integron_finder is free software: you can redistribute it and/or modify
#10 1.424 it under the terms of the GNU General Public License as published by
#10 1.424 the Free Software Foundation, either version 3 of the License, or
#10 1.424 (at your option) any later version.
#10 1.424 
#10 1.424 integron_finder is distributed in the hope that it will be useful,
#10 1.424 but WITHOUT ANY WARRANTY; without even the implied warranty of
#10 1.424 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#10 1.424 GNU General Public License for more details.
#10 1.424 
#10 1.424 You should have received a copy of the GNU General Public License
#10 1.424 along with this program (COPYING file).
#10 1.424 If not, see <http://www.gnu.org/licenses/>.
#10 1.424 
#10 1.424                      =======================
#10 1.424 
#10 1.424 command used: integron_finder --local-max --circ --keep-tmp NZ_CP01[632](https://github.com/StaPH-B/docker-builds/actions/runs/11112552704/job/30874906925?pr=1074#step:8:638)3.fna
#10 1.424 
#10 1.424                      =======================
#10 1.424 
#10 1.424 
#10 1.428 INFO     :  ############ Processing replicon NZ_CP016323.1 (1/1) ############
#10 1.428 
#10 1.525 INFO     :  Starting Default search ... :
#10 2.196 INFO     :  Default search done... : 
#10 2.360 INFO     :  In replicon NZ_CP016323.1, there are:
#10 2.360 INFO     :  - 0 complete integron(s) found with a total 0 attC site(s)
#10 2.360 INFO     :  - 2 CALIN element(s) found with a total of 44 attC site(s)
#10 2.360 INFO     :  - 0 In0 element(s) found with a total of 0 attC site
#10 2.360 INFO     :  Starting search with local_max...:
#10 13.76 INFO     :    searched 35181->39381 in bottom strand(s) found 0 attc sites
#10 28.74 INFO     :    searched 11266->15466 in bottom strand(s) found 0 attc sites
#10 28.75 INFO     :  Search with local_max done... :
#10 28.90 INFO     :  In replicon NZ_CP016323.1, there are:
#10 28.90 INFO     :  - 0 complete integron(s) found with a total 0 attC site(s)
#10 28.90 INFO     :  - 2 CALIN element(s) found with a total of 46 attC site(s)
#10 28.90 INFO     :  - 0 In0 element(s) found with a total of 0 attC site
#10 28.90 INFO     :  Adding proteins ... :
#10 29.00 INFO     :  Adding proteins ... :
#10 29.06 INFO     :  Writing out results for replicon NZ_CP016323.1
#10 29.08 INFO     :  Merging integrons results.
#10 29.08 
#10 29.17 # integron_finder 2.0.5 
#10 29.17 # cmd: integron_finder --local-max --circ --keep-tmp NZ_CP016323.fna
#10 29.17 ID_replicon   CALIN   complete    In0 topology    size
#10 29.17 NZ_CP016323.1 2   0   0   circ    40850
#10 29.17 # integron_finder 2.0.5 
#10 29.17 # cmd: integron_finder --local-max --circ --keep-tmp NZ_CP016323.fna
#10 29.17 ID_integron   ID_replicon element pos_beg pos_end strand  evalue  type_elt    annotation  model   type    default distance_2attC  considered_topology
#10 29.17 integron_01   NZ_CP016323.1   NZ_CP016323.1_3 1207    1[638](https://github.com/StaPH-B/docker-builds/actions/runs/11112552704/job/30874906925?pr=1074#step:8:644)    -1  NA  protein protein NA  CALIN   No  NA  circ
#10 29.17 integron_01   NZ_CP016323.1   NZ_CP016323.1_4 1669    1857    1   NA  protein protein NA  CALIN   No  NA  circ
#10 29.17 integron_01   NZ_CP016323.1   attc_001    1733    1859    1   0.00026 attC    attC    attc_4  CALIN   No  NA  circ
#10 29.17 integron_01   NZ_CP016323.1   attc_002    2331    2457    1   7.7e-06 attC    attC    attc_4  CALIN   No  472.0   circ
#10 29.17 integron_01   NZ_CP016323.1   NZ_CP016323.1_5 2481    3233    1   NA  protein protein NA  CALIN   No  NA  circ
#10 29.17 integron_01   NZ_CP016323.1   attc_003    3233    3360    1   1.4e-05 attC    attC    attc_4  CALIN   No  776.0   circ
#10 29.17 integron_01   NZ_CP016323.1   NZ_CP016323.1_6 3880    4704    -1  NA  protein protein NA  CALIN   No  NA  circ
#10 DONE 29.2s

erinyoung commented 2 weeks ago

Thank you for putting this together!

You can check the status of the deploy here : https://github.com/StaPH-B/docker-builds/actions/runs/11147334197

StaPH-B / docker-builds

adds integron finder #1074