Update assembly_eval tool versions, add seqkit

Author: jwertz01

assembly_eval/0.5/Dockerfile

@@ -0,0 +1,21 @@
+FROM continuumio/miniconda3
+
+MAINTAINER Eichler Lab
+
+COPY ./environment.yml /
+
+RUN conda env create -f /environment.yml && conda clean -a
+
+ENV PATH=/opt/conda/envs/assembly_eval/bin/:${PATH}
+
+RUN apt-get -y update && apt-get -y install file gawk && ln -sf /usr/bin/gawk /usr/bin/awk
+
+ENV LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/opt/conda/envs/assembly_eval/lib/
+
+RUN echo "source activate assembly_eval" > ~/.bashrc
+
+RUN mkdir -p /app/
+
+ENV CURL_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt
+
+COPY ./software.list /app/

assembly_eval/0.5/environment.yml

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+name: assembly_eval
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - samtools
+  - minimap2
+  - winnowmap
+  - meryl
+  - bedtools
+  - rustybam
+  - repeatmasker
+  - rsync
+  - seqkit
+prefix: /opt/conda/envs/assembly_eval

assembly_eval/0.5/software.list

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+samtools=1.23
+minimap2=2.30
+bedtools=2.31.1
+winnowmap=2.03
+meryl=1.4.1
+rustybam=0.1.34
+repeatmasker=4.2.2
+seqkit=1.23