8000 Papd 18 change external references to eit by JDhillonEIT · Pull Request #1 · EIT-Pathogena/hostile-eit · GitHub
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Papd 18 change external references to eit #1

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Merged
merged 10 commits into from
Jul 22, 2024
Merged

Papd 18 change external references to eit #1

merged 10 commits into from
Jul 22, 2024

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JDhillonEIT
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@JDhillonEIT JDhillonEIT commented Jul 17, 2024 •
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Similar to the Client changes, I've bumped the version in use here to signify a breaking change in the bucket reference links and to break from the current versioning.

I've also incorporated the changes we're currently using in Hostile-S3 so this would then supersede that repo.

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Additional testing

  • Confirmed hostile fetch can pull the index files to a new hostile-eit application folder. Users can copy across their local files instead of re-downloading if they wish.

  • Installed in a local Pathogena Client Conda environment and ran hostile on fastq files

16:15:19 INFO: EIT Pathogena client version 2.0.0rc1
16:15:19 INFO: Performing FastQ checks and gathering total reads
16:15:19 INFO: Calculating read count in: /Users/jdhillon/code/pathogena/client/tests/data/reads/tuberculosis_1_1.fastq
16:15:19 INFO: Calculating read count in: /Users/jdhillon/code/pathogena/client/tests/data/reads/tuberculosis_1_2.fastq
16:15:19 INFO: 2.0 reads in FASTQ file
16:15:19 INFO: Removing human reads from ILLUMINA FastQ files and storing in /Users/jdhillon/code/pathogena/client
16:15:19 INFO: Hostile version 2.0.0rc1. Mode: paired short read (Bowtie2)
16:15:19 INFO: Fetching standard index human-t2t-hla-argos985-mycob140 (https://objectstorage.uk-london-1.oraclecloud.com/n/lr3yhdniv6gu/b/human-genome-indices/o/human-t2t-hla-argos985-mycob140.tar)
100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 4.24G/4.24G [12:55<00:00, 5.87MB/s]
16:28:15 INFO: Verifying checksum be0d63ed39d9eeb9657e936c3ded7661c1ef64d8a0de3c1acaf92348c9c8993d…
16:28:25 INFO: Extracting human-t2t-hla-argos985-mycob140.tar…
16:28:28 INFO: Downloaded standard index /Users/jdhillon/Library/Application Support/hostile-eit/human-t2t-hla-argos985-mycob140
16:28:28 INFO: Cleaning…
16:28:29 INFO: Cleaning complete
16:28:29 INFO: Human reads removed from input samples and can be found here: /Users/jdhillon/code/pathogena/client
  • Tested pathogena upload with an Illumina sample with human read removal|decontamination enabled (sample)
16:48:01 INFO: EIT Pathogena client version 2.0.0rc1
16:48:02 INFO: Removing human reads from ILLUMINA FastQ files and storing in /Users/jdhillon/code/pathogena/client
16:48:02 INFO: Hostile version 2.0.0rc1. Mode: paired short read (Bowtie2)
16:48:02 INFO: Found cached standard index human-t2t-hla-argos985-mycob140
16:48:02 INFO: Cleaning…
16:48:29 INFO: Cleaning complete
16:48:29 INFO: Human reads removed from input samples and can be found here: /Users/jdhillon/code/pathogena/client
16:48:31 INFO: Uploading sample1-jay
16:51:43 INFO:   Uploaded ab40758e-5161-46c7-b0ec-8c054a29c218_1.fastq.gz
16:51:43 INFO: Uploading sample1-jay
16:55:09 INFO:   Uploaded ab40758e-5161-46c7-b0ec-8c054a29c218_2.fastq.gz
16:55:09 INFO: Upload complete. Created uzyw9b.mapping.csv (keep this safe)

JDhillonEIT
JDhillonEIT commented Jul 18, 2024
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@JDhillonEIT JDhillonEIT self-assigned this Jul 18, 2024
ngochieu642
ngochieu642 suggested changes Jul 19, 2024
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Overall looks good to me. Just need to handle some minor syntax in github action script

@ngochieu642
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And could you please double check the following things:

  • We have a secret OCI_USERNAME_GPASLTD
  • We have a secret OCI_TOKEN_GPASLTD
  • The username & token can be used to push to gpasltd
  • There is already a hostile-eit inside gpasltd, we must create this prior to the push, otherwise it will result in some errors

@JDhillonEIT @ngochieu642
Apply suggestions from code review
63afc6a 
Fixes in the workflow actions picked up by Hieu.

Co-authored-by: Hieu Thai <hieuthai642@gmail.com>
@JDhillonEIT
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And could you please double check the following things:

  • We have a secret OCI_USERNAME_GPASLTD
  • We have a secret OCI_TOKEN_GPASLTD
  • The username & token can be used to push to gpasltd
  • There is already a hostile-eit inside gpasltd, we must create this prior to the push, otherwise it will result in some errors

I can confirm these exist and I've tested logging into the registry with these credentials:
image

I've created hostile-eit inside OCIR

image

@JDhillonEIT JDhillonEIT merged commit a67a586 into main Jul 22, 2024
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@JDhillonEIT JDhillonEIT deleted the PAPD-18-Change-external-references-to-EIT branch July 22, 2024 14:29
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