diff --git a/Dockerfile b/Dockerfile index 45d7477..84297fb 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,9 +1,8 @@ -FROM debian:jessie -MAINTAINER Sam Minot +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 && \ @@ -11,9 +10,9 @@ RUN git clone https://github.com/sstephenson/bats.git /tmp/bats && \ # 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 \ No newline at end of file +RUN bats /tmp/test diff --git a/requirements.txt b/requirements.txt index 1a3ed7b..849b618 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,3 +1,3 @@ # Python dependencies installed in Dockerfile -onecodex==0.2.0a1 -awscli==1.8.3 \ No newline at end of file +onecodex +awscli diff --git a/test/ocx.bats b/test/ocx.bats index 0bb2799..719cd8a 100644 --- a/test/ocx.bats +++ b/test/ocx.bats @@ -1,13 +1,13 @@ #!/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" { @@ -15,22 +15,22 @@ [[ $F == *2.8.0* ]] } -@test "AWS CLI 1.8.3" { +@test "AWS CLI" { X=$(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* ]] -} \ No newline at end of file +}