onecodex · audy · Dec 8, 2025
diff --git a/Dockerfile b/Dockerfile
@@ -1,19 +1,18 @@
-FROM debian:jessie
-MAINTAINER Sam Minot <sam@onecodex.com>
+FROM ubuntu

 # Update and install Python
 RUN apt-get update -y
-RUN apt-get install -y python python-pip curl wget git pigz
+RUN apt-get install -y python3 python3-pip curl wget git pigz

 # Install Bats
 RUN git clone https://github.com/sstephenson/bats.git /tmp/bats && \
    cd /tmp/bats && ./install.sh /usr/local

 # Install requirements.txt (One Codex CLI)
 ADD requirements.txt /tmp/requirements.txt
-RUN pip install -r /tmp/requirements.txt && rm /tmp/requirements.txt
+RUN pip install -r /tmp/requirements.txt --break-system-packages && rm /tmp/requirements.txt

-# Add the AWS CLI binaries
+# Add the SRA toolkit binaries
 RUN cd /tmp && \
    wget http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.8.0/sratoolkit.2.8.0-ubuntu64.tar.gz && \
    tar xzvf sratoolkit.2.8.0-ubuntu64.tar.gz && \
@@ -24,4 +23,4 @@ ADD https://gist.githubusercontent.com/boydgreenfield/805ac27e0a6b9a5adea7/raw/e

 # Integration tests
 ADD test /tmp/test
-RUN bats /tmp/test
+RUN bats /tmp/test
diff --git a/requirements.txt b/requirements.txt
@@ -1,3 +1,3 @@
 # Python dependencies installed in Dockerfile
-onecodex==0.2.0a1
-awscli==1.8.3
+onecodex
+awscli
diff --git a/test/ocx.bats b/test/ocx.bats
@@ -1,36 +1,36 @@
 #!/usr/bin/env bats

-@test "Python 2.7.X should be installed" {
-    V=$(python --version 2>&1)
-    [[ $V == Python\ 2.7* ]]
+@test "Python 3 should be installed" {
+    V=$(python3 --version 2>&1)
+    [[ $V == Python\ 3* ]]
 }

 @test "Pigz installed" {
    V=$(pigz --version 2>&1)
-    [[ $V == pigz\ 2.3* ]]
+    [[ $V == pigz* ]]
 }

 @test "fastq-dump v2.8.0" {
    F=$(fastq-dump --version)
    [[ $F == *2.8.0* ]]
 }

-@test "AWS CLI 1.8.3" {
+@test "AWS CLI" {
    X=$(aws --version 2>&1)
-    [[ $X == *aws-cli/1.8.3* ]]
+    [[ $X == *aws-cli* ]]
 }

-@test "One Codex CLI v0.2.0a1" {
+@test "One Codex CLI" {
    X=$(onecodex --version 2>&1)
-    [[ $X == *0.2.0-alpha1* ]]
+    [[ $X == *onecodex* ]]
 }

 @test "Join paired ends script exists" {
-    X=$(python /scripts/join_paired_ends.py --help)
+    X=$(python3 /scripts/join_paired_ends.py --help)
    [[ $X == *Join\ two\ FASTQ\ paired\ end\ read\ files.* ]]
 }

 @test "Join paired ends script supports interleaving" {
-    X=$(python /scripts/join_paired_ends.py --help)
+    X=$(python3 /scripts/join_paired_ends.py --help)
    [[ $X == *interleave* ]]
-}
+}