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Welcome to 2025 #2

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11 changes: 5 additions & 6 deletions Dockerfile
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Original file line number Diff line number Diff line change
@@ -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 && \
Expand All @@ -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
4 changes: 2 additions & 2 deletions requirements.txt
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@@ -1,3 +1,3 @@
# Python dependencies installed in Dockerfile
onecodex==0.2.0a1
awscli==1.8.3
onecodex
awscli
22 changes: 11 additions & 11 deletions test/ocx.bats
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@@ -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* ]]
}
}