add step to extract taxonomy from gs_tsv

DessimozLab · Aug 14, 2024 · ab3ee68 · ab3ee68
1 parent 781b0c3
commit ab3ee68
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Showing 6 changed files with 482 additions and 408 deletions.
diff --git a/containers/oma/Dockerfile b/containers/oma/Dockerfile
@@ -1,10 +1,9 @@
-FROM python:3.11-slim as basis
+FROM python:3.11-slim AS basis
 
 # set environment varibles
-#ENV PYTHONDONTWRITEBYTECODE 1
-ENV PYTHONUNBUFFERED 1
+ENV PYTHONUNBUFFERED=1
 
-FROM basis as builder
+FROM basis AS builder
 RUN apt-get update \
     && apt-get install -y --no-install-recommends \
        build-essential \
@@ -32,7 +31,7 @@ RUN --mount=type=ssh \
     LABGIT=$(cat /run/secrets/labgit ) \
        pipenv sync
 
-FROM basis as runtime
+FROM basis AS runtime
 RUN apt-get update \
     && apt-get install -y --no-install-recommends \
        libxml2 \

diff --git a/containers/oma/Pipfile b/containers/oma/Pipfile
@@ -8,9 +8,11 @@ omahdf5tordf = {git = "git+${LABGIT}/biosoda"}
 omamer = "*"
 edgehog = "*"
 hogprop = {git = "git+${LABGIT}/hogprop2"}
-         #branch = "nf-convert", 
-#pyoma = {git = "git+https://github.com/DessimozLab/pyoma.git", ref = "v0.13.3", extras = ["create_db", "enrichment", "notebooks"] }
+         #branch = "nf-convert",
+         #ref = "v0.13.3"
+#pyoma = {git = "git+https://github.com/DessimozLab/pyoma.git", branch = "nf-convert", extras = ["create_db", "enrichment", "notebooks"] }
 pyoma = "*"
+omataxonomy = "*"
 
 [dev-packages]