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Dram1.4rc #207

Merged
merged 72 commits into from
Sep 28, 2022
Merged

Dram1.4rc #207

merged 72 commits into from
Sep 28, 2022

Commits on Mar 1, 2022

  1. dbcan: ++ best hits, subfam ec numbers columns change cutoff to 1e-18

    @rmFlynn
    rmFlynn committed Mar 1, 2022
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Commits on Mar 3, 2022

  1. fix up downloads, for dbcan and others

    @rmFlynn
    rmFlynn committed Mar 3, 2022
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Commits on Mar 4, 2022

  1. Finish up download, and setup

    @rmFlynn
    rmFlynn committed Mar 4, 2022
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Commits on Mar 7, 2022

  1. Merge branch 'master' into dbcan_fix

    Rory M Flynn committed Mar 7, 2022
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Commits on Apr 6, 2022

  1. Check that ECs go through the full pipeline.

    Rory M Flynn committed Apr 6, 2022
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Commits on Apr 25, 2022

  1. Add the first logging attempt

    Rory M Flynn committed Apr 25, 2022
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  2. Stuff for logging, move code in cmd to facilitate

    Rory M Flynn committed Apr 25, 2022
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  3. change log file

    Rory M Flynn committed Apr 25, 2022
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Commits on May 2, 2022

  1. changed print statements to logging.info and removed start_time on cm… 

    …d function
    @ileleiwi
    ileleiwi committed May 2, 2022
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  2. fixed setup_logger call

    @ileleiwi
    ileleiwi committed May 2, 2022
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  3. added an output directory for log and replaced all print statements i… 

    …n print_database_locations with logging.info
    @ileleiwi
    ileleiwi committed May 2, 2022
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  4. added logging to prepare_databases

    @ileleiwi
    ileleiwi committed May 2, 2022
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  5. added logging and logging.info messages where files are written out i… 

    …n get_gene_neighborhoods
    @ileleiwi
    ileleiwi committed May 2, 2022
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  6. Add one doc string

    Rory M Flynn committed May 2, 2022
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Commits on May 5, 2022

  1. Fix ec numbers, fully add camper, updating

    Rory M Flynn committed May 5, 2022
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Commits on May 24, 2022

  1. Merge branch 'dram1.4_leleiwi' into dbcan_fix

    Rory M Flynn committed May 24, 2022
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  2. add new config

    Rory M Flynn committed May 24, 2022
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  3. BIO: Add in dbcan_fix 

     The important thing to know is that I think the count should be per gene, not per genome. They are called internally in dram but they are genes. So if there is one gene in a genome with AA1_2;AA1_3 that is a count of one in the distillate, if there is another gene with say AA1_4;AA1_5;AA1_2  on another line of the annotations, then each AA1_2;AA1_3  and AA1_4;AA1_5;AA1_2 would count for 1 and AA1 would have a count of 2.
    Rory M Flynn committed May 24, 2022
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Commits on May 31, 2022

  1. Add camper, and genie and also add logging

    Rory M Flynn committed May 31, 2022
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Commits on Jun 3, 2022

  1. small bug fixes, missing arguments, ext

    Rory M Flynn committed Jun 3, 2022
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  2. need to add back in the locs

    Rory M Flynn committed Jun 3, 2022
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Commits on Jun 7, 2022

  1. Finished most of the setup bugs

    Rory M Flynn committed Jun 7, 2022
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Commits on Jun 10, 2022

  1. less bugs

    Rory M Flynn committed Jun 10, 2022
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  2. Less bugs

    Rory M Flynn committed Jun 10, 2022
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  3. Merge branch 'dbcan_fix' into finalize_setup

    Rory M Flynn committed Jun 10, 2022
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Commits on Jun 20, 2022

  1. Chrush bugs, logging for distill, sulphur placeholder

    Rory M Flynn committed Jun 20, 2022
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Commits on Jun 24, 2022

  1. Start the process of fixing tests, validating

    Rory M Flynn committed Jun 24, 2022
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  2. Now sulphur place holder is inplace

    Rory M Flynn committed Jun 24, 2022
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  3. Sulpher stuff and bugs

    Rory M Flynn committed Jun 24, 2022
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Commits on Jun 27, 2022

  1. add log back

    Rory M Flynn committed Jun 27, 2022
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Commits on Jun 28, 2022

  1. Fix update descriptions

    Rory M Flynn committed Jun 28, 2022
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Commits on Jul 5, 2022

  1. working updates

    Rory M Flynn committed Jul 5, 2022
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  2. Debuging tweeks

    Rory M Flynn committed Jul 5, 2022
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Commits on Jul 8, 2022

  1. so many bugs patched

    Rory M Flynn committed Jul 8, 2022
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Commits on Jul 27, 2022

  1. Fix all tests, add adjectives to strainer

    Rory M Flynn committed Jul 27, 2022
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  2. Enable all databases

    Rory M Flynn committed Jul 27, 2022
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  3. add sulphur

    Rory M Flynn committed Jul 27, 2022
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Commits on Jul 28, 2022

  1. Remove campers but now I need to add it back to the distillate

    Rory M Flynn committed Jul 28, 2022
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Commits on Aug 4, 2022

  1. Fix some test

    Rory M Flynn committed Aug 4, 2022
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Commits on Aug 10, 2022

  1. Merge branch 'scikit_fix' into dbcan_fix

    Rory M Flynn committed Aug 10, 2022
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Commits on Aug 15, 2022

  1. Read config location from environment variable

    @merrygoat
    merrygoat committed Aug 15, 2022
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Commits on Aug 31, 2022

  1. Remove customs and fix tests

    Rory M Flynn committed Aug 31, 2022
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  2. Merge pull request #202 from merrygoat/custom_config_location 

    Read config location from environment variable
    @rmFlynn
    rmFlynn authored Aug 31, 2022
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  3. Git the package fix in circleci

    Rory M Flynn committed Aug 31, 2022
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  4. fix one test

    Rory M Flynn committed Aug 31, 2022
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Commits on Sep 1, 2022

  1. Change all FTP URLs to HTTP(s) to avoid firewall/ACL issues

    @mrobbert
    mrobbert committed Sep 1, 2022
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Commits on Sep 2, 2022

  1. Fix lib call and add config path test

    Rory M Flynn committed Sep 2, 2022
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  2. Merge branch 'master' into dram1.4rc

    @rmFlynn
    rmFlynn authored Sep 2, 2022
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Commits on Sep 9, 2022

  1. Merge branch 'add_http_option' into master

    @rmFlynn
    rmFlynn authored Sep 9, 2022
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  2. Merge pull request #206 from mrobbert/master 

    Change all FTP URLs to HTTP(s) to avoid firewall/ACL issues
    @rmFlynn
    rmFlynn authored Sep 9, 2022
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  3. Literally deleted one trailing space

    Rory M Flynn committed Sep 9, 2022
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Commits on Sep 12, 2022

  1. Add the option for https or any alt link in download

    Rory M Flynn committed Sep 12, 2022
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Commits on Sep 14, 2022

  1. clean the code a touch for release

    Rory M Flynn committed Sep 14, 2022
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  2. Merge branch 'add_http_option' into dram1.4rc

    Rory M Flynn committed Sep 14, 2022
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  3. I am once again asking for circleci to run

    Rory M Flynn committed Sep 14, 2022
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  4. tweek config

    @rmFlynn
    rmFlynn authored Sep 14, 2022
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Commits on Sep 15, 2022

  1. Updated config.yml

    @rmFlynn
    rmFlynn committed Sep 15, 2022
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  2. Updated config.yml

    @rmFlynn
    rmFlynn committed Sep 15, 2022
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  3. Updated config.yml

    @rmFlynn
    rmFlynn committed Sep 15, 2022
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  4. Updated config.yml

    @rmFlynn
    rmFlynn committed Sep 15, 2022
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  5. Updated config.yml

    @rmFlynn
    rmFlynn committed Sep 15, 2022
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  6. Updated config.yml

    @rmFlynn
    rmFlynn committed Sep 15, 2022
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  7. Updated config.yml

    @rmFlynn
    rmFlynn committed Sep 15, 2022
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  8. Updated config.yml

    @rmFlynn
    rmFlynn committed Sep 15, 2022
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  9. Bump dbcan to 11

    Rory M Flynn committed Sep 15, 2022
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Commits on Sep 22, 2022

  1. Bring public DRAM up to speck, with in house

    Rory M Flynn committed Sep 22, 2022
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  2. Remove Sulphur legacy from distilate

    Rory M Flynn committed Sep 22, 2022
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  3. Fix one test for one less log

    Rory M Flynn committed Sep 22, 2022
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  4. Tweak version

    Rory M Flynn committed Sep 22, 2022
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Commits on Sep 26, 2022

  1. Last minute edits

    Rory M Flynn committed Sep 26, 2022
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Commits on Sep 28, 2022

  1. Remove some todos and add citation

    Rory M Flynn committed Sep 28, 2022
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  2. Update README

    Rory M Flynn committed Sep 28, 2022
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