first commit

data/sample_mbelari.csv

+female1: data/Mbelari_females/1_S1_L001_R1_001.fastq.gz ; data/Mbelari_females/1_S1_L001_R2_001.fastq.gz
+female2: data/Mbelari_females/2_S2_L001_R1_001.fastq.gz ; data/Mbelari_females/2_S2_L001_R2_001.fastq.gz
+female3: data/Mbelari_females/3_S3_L001_R1_001.fastq.gz ; data/Mbelari_females/3_S3_L001_R2_001.fastq.gz
+female4: data/Mbelari_females/4_S4_L001_R1_001.fastq.gz ; data/Mbelari_females/4_S4_L001_R2_001.fastq.gz
+female5: data/Mbelari_females/5_S5_L001_R1_001.fastq.gz ; data/Mbelari_females/5_S5_L001_R2_001.fastq.gz
+female6: data/Mbelari_females/6_S6_L001_R1_001.fastq.gz ; data/Mbelari_females/6_S6_L001_R2_001.fastq.gz
+female7: data/Mbelari_females/MRDR5_R1.fastq.gz ; data/Mbelari_females/MRDR5_R2.fastq.gz
+male1: /data/Mbelari_males/JU2817_males_S11_L002_R1_001.fastq.gz ; /data/Mbelari_males/JU2817_males_S11_L002_R2_001.fastq.gz
+male2: /data/Mbelari_males/MRDR6_R1.fastq.gz ; /data/Mbelari_males/MRDR6_R2.fastq.gz

data/sample_mlongespiculosa.csv

+female1: data/Mlongespiculosa/MRDR3_R1.fastq.gz ; data/Mlongespiculosa/MRDR3_R2.fastq.gz
+male1: /data/Mlongespiculosa/MRDR4_R1.fastq.gz ; /data/Mlongespiculosa/MRDR4_R1.fastq.gz

data/sample_mspiculigera.csv

+female1: data/Mlongespiculosa/AF72-females_BIS_S8_L002_R1_001.fastq.gz ; data/Mlongespiculosa/AF72-females_BIS_S8_L002_R2_001.fastq.gz
+male1: /data/Mlongespiculosa/AF72-males_S7_L002_R1_001.fastq.gz ; /data/Mlongespiculosa/AF72-males_S7_L002_R2_001.fastq.gz
+

src/Dockerfile

+FROM ubuntu:22.04
+
+RUN apt update \
+  && apt install -y git libgsl-dev libopenblas-dev liblapacke-dev libbz2-dev zlib1g-dev zlib1g cmake gcc g++ \
+  && git clone --recursive https://github.com/tlemane/kmdiff \
+  && cd kmdiff \
+  && ./install.sh \
+  && cp kmdiff_build/bin/* /usr/bin/ \
+  && cd / \
+  && rm -Rf kmdiff
+

src/kmdiff.sh

+# build docker image
+docker build src/ -t 'lbmc/kmdiff:1.0.1'
+docker push lbmc/kmdiff:1.0.1
+
+# build charliecloud image
+ch-image pull -s /Xnfs/abc/charliecloud/ lbmc/kmdiff:1.0.1
+update_ch_image.sh
+
+alias kmdiff="ch-run -b /scratch /Xnfs/abc/charliecloud/img/lbmc%kmdiff+1.0.1 -- kmdiff"
+
+# kmdiff count
+
+kmdiff count -f data/sample_mbelari.csv -d results/mbelari_counts/ -t 32
+kmdiff count -f data/sample_mlongespiculosa.csv -d results/mlongespiculosa_counts/ -t 32
+kmdiff count -f data/sample_mspiculigera.csv -d results/mspiculigera_counts/ -t 32