From 54e9308e8fed970f47a49343186a7dc0f4a860e6 Mon Sep 17 00:00:00 2001 From: bbimber Date: Sun, 25 Jan 2026 14:41:06 -0800 Subject: [PATCH 1/7] Bugfix to docker --- containers/cat/Dockerfile | 48 +++++++++++++++++++-------------------- 1 file changed, 23 insertions(+), 25 deletions(-) diff --git a/containers/cat/Dockerfile b/containers/cat/Dockerfile index 33659d8..cf6e1ec 100644 --- a/containers/cat/Dockerfile +++ b/containers/cat/Dockerfile @@ -4,32 +4,27 @@ ARG AUGUSTUS_COMMIT=36ae43d #RUN add-apt-repository -y ppa:deadsnakes/ppa RUN apt-get update \ - && apt-get install -y libcurl4-openssl-dev - -RUN apt-get install -y libcurl4-gnutls-dev - -RUN apt-get install --fix-missing -y build-essential libssl-dev libncurses5-dev libcurl4-openssl-dev liblzma-dev libbz2-dev \ + && apt-get install --fix-missing -y build-essential libssl-dev libncurses5-dev libcurl4-openssl-dev liblzma-dev libbz2-dev \ libboost-all-dev sqlite3 libsqlite3-0 libsqlite3-dev libgsl0-dev lp-solve liblpsolve55-dev libbamtools-dev wget git \ - wget bedtools bamtools samtools sqlite3 libgsl0-dev libcolamd2 libcurl4-openssl-dev exonerate \ + wget bedtools bamtools samtools sqlite3 libgsl0-dev libcolamd2 libcurl4-openssl-dev exonerate augustus augustus-data augustus-doc \ samtools bcftools libhdf5-dev libbigwig-dev \ && apt-get install -y libhts-dev -# missing packages: software-properties-common -RUN apt install -y augustus augustus-data augustus-doc - ## htslib -RUN git clone --recursive https://github.com/samtools/htslib.git -RUN cd htslib && make install +RUN git clone --recursive https://github.com/samtools/htslib.git \ + && cd htslib \ + && make install ## bcftools -RUN git clone https://github.com/samtools/bcftools.git -RUN cd bcftools && make +RUN git clone https://github.com/samtools/bcftools.git \ + && cd bcftools \ + && make ## samtools -RUN git clone https://github.com/samtools/samtools -RUN cd samtools \ - && make \ - && make install +RUN git clone https://github.com/samtools/samtools \ + && cd samtools \ + && make \ + && make install ## MOVE Directories INTO $HOME/tool RUN mkdir /root/tools \ @@ -69,13 +64,16 @@ RUN git clone https://github.com/dahlo/WiggleTools #RUN cd WiggleTools && make \ # && cp /WiggleTools/bin/* /bin/ -RUN conda create -y -n cat -c conda-forge -c bioconda -c defaults python=3.7 pyfasta luigi seaborn pandas \ - ete3 pysam numpy scipy bx-python bcbio-gff biopython parasail-python configobj sqlalchemy \ - samtools bamtools augustus exonerate wiggletools bedtools \ - ucsc-fatotwobit ucsc-gff3togenepred ucsc-genepredtobed ucsc-genepredtofakepsl ucsc-bamtopsl ucsc-transmappsltogenepred \ - ucsc-pslpostarget ucsc-axtchain ucsc-chainmergesort ucsc-pslmap ucsc-pslrecalcmatch ucsc-pslmappostchain \ - ucsc-gtftogenepred ucsc-genepredtogtf ucsc-pslcdnafilter ucsc-psltobigpsl \ - ucsc-bedsort ucsc-bedtobigbed ucsc-fasize ucsc-wigtobigwig ucsc-hgloadchain +RUN conda create -y -n cat -c conda-forge -c bioconda -c defaults python=3.7 \ + && source activate cat \ + && python3 --version \ + && python3 -m pip install -y pyfasta luigi seaborn pandas \ + ete3 pysam numpy scipy bx-python bcbio-gff biopython parasail-python configobj sqlalchemy \ + samtools bamtools augustus exonerate wiggletools bedtools \ + ucsc-fatotwobit ucsc-gff3togenepred ucsc-genepredtobed ucsc-genepredtofakepsl ucsc-bamtopsl ucsc-transmappsltogenepred \ + ucsc-pslpostarget ucsc-axtchain ucsc-chainmergesort ucsc-pslmap ucsc-pslrecalcmatch ucsc-pslmappostchain \ + ucsc-gtftogenepred ucsc-genepredtogtf ucsc-pslcdnafilter ucsc-psltobigpsl \ + ucsc-bedsort ucsc-bedtobigbed ucsc-fasize ucsc-wigtobigwig ucsc-hgloadchain RUN source activate cat \ && python3 -m pip install git+https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit.git @@ -83,7 +81,7 @@ RUN source activate cat \ RUN python3 --version RUN source activate cat \ - python3 --version \ + python3 --version RUN mkdir -p /augustus \ && git clone https://github.com/Gaius-Augustus/Augustus.git \ From 558133d36af25fb8a5155178ae1468c73b731c18 Mon Sep 17 00:00:00 2001 From: bbimber Date: Sun, 25 Jan 2026 15:32:58 -0800 Subject: [PATCH 2/7] Bugfix to docker --- containers/cat/Dockerfile | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/containers/cat/Dockerfile b/containers/cat/Dockerfile index cf6e1ec..927a552 100644 --- a/containers/cat/Dockerfile +++ b/containers/cat/Dockerfile @@ -61,13 +61,15 @@ RUN wget -q https://github.com/biod/sambamba/releases/download/v0.6.7/sambamba_v # WiggleTools RUN git clone https://github.com/dahlo/WiggleTools -#RUN cd WiggleTools && make \ +# && cd WiggleTools && make \ # && cp /WiggleTools/bin/* /bin/ -RUN conda create -y -n cat -c conda-forge -c bioconda -c defaults python=3.7 \ - && source activate cat \ - && python3 --version \ - && python3 -m pip install -y pyfasta luigi seaborn pandas \ +RUN conda create -y -n cat python=3.7 \ + && echo "conda activate cat" >> ~/.bashrc + +RUN python3 --version \ + && conda install -c conda-forge -c bioconda -c defaults -y \ + pyfasta luigi seaborn pandas \ ete3 pysam numpy scipy bx-python bcbio-gff biopython parasail-python configobj sqlalchemy \ samtools bamtools augustus exonerate wiggletools bedtools \ ucsc-fatotwobit ucsc-gff3togenepred ucsc-genepredtobed ucsc-genepredtofakepsl ucsc-bamtopsl ucsc-transmappsltogenepred \ @@ -75,12 +77,12 @@ RUN conda create -y -n cat -c conda-forge -c bioconda -c defaults python=3.7 \ ucsc-gtftogenepred ucsc-genepredtogtf ucsc-pslcdnafilter ucsc-psltobigpsl \ ucsc-bedsort ucsc-bedtobigbed ucsc-fasize ucsc-wigtobigwig ucsc-hgloadchain -RUN source activate cat \ +RUN conda init && conda activate cat \ && python3 -m pip install git+https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit.git RUN python3 --version -RUN source activate cat \ +RUN conda init && conda activate cat \ python3 --version RUN mkdir -p /augustus \ From 8038f3a01c2533c456699bd6f65f4e50360f1c5f Mon Sep 17 00:00:00 2001 From: bbimber Date: Sun, 25 Jan 2026 15:33:34 -0800 Subject: [PATCH 3/7] Bugfix to docker --- containers/cat/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/containers/cat/Dockerfile b/containers/cat/Dockerfile index 927a552..a64a59d 100644 --- a/containers/cat/Dockerfile +++ b/containers/cat/Dockerfile @@ -77,12 +77,12 @@ RUN python3 --version \ ucsc-gtftogenepred ucsc-genepredtogtf ucsc-pslcdnafilter ucsc-psltobigpsl \ ucsc-bedsort ucsc-bedtobigbed ucsc-fasize ucsc-wigtobigwig ucsc-hgloadchain -RUN conda init && conda activate cat \ +RUN conda activate cat \ && python3 -m pip install git+https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit.git RUN python3 --version -RUN conda init && conda activate cat \ +RUN conda activate cat \ python3 --version RUN mkdir -p /augustus \ From cfdd262bd034410e20445b504423ecad3f9b36dd Mon Sep 17 00:00:00 2001 From: bbimber Date: Sun, 25 Jan 2026 15:43:32 -0800 Subject: [PATCH 4/7] Bugfix to docker --- containers/cat/Dockerfile | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/containers/cat/Dockerfile b/containers/cat/Dockerfile index a64a59d..5f88d2f 100644 --- a/containers/cat/Dockerfile +++ b/containers/cat/Dockerfile @@ -67,8 +67,7 @@ RUN git clone https://github.com/dahlo/WiggleTools RUN conda create -y -n cat python=3.7 \ && echo "conda activate cat" >> ~/.bashrc -RUN python3 --version \ - && conda install -c conda-forge -c bioconda -c defaults -y \ +RUN conda install -n cat -c conda-forge -c bioconda -c defaults -y \ pyfasta luigi seaborn pandas \ ete3 pysam numpy scipy bx-python bcbio-gff biopython parasail-python configobj sqlalchemy \ samtools bamtools augustus exonerate wiggletools bedtools \ @@ -78,7 +77,7 @@ RUN python3 --version \ ucsc-bedsort ucsc-bedtobigbed ucsc-fasize ucsc-wigtobigwig ucsc-hgloadchain RUN conda activate cat \ - && python3 -m pip install git+https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit.git + && conda install -n cat -y git+https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit.git RUN python3 --version From f91838fd84498cdac19ba33273fdfe123ead7604 Mon Sep 17 00:00:00 2001 From: bbimber Date: Sun, 25 Jan 2026 18:53:25 -0800 Subject: [PATCH 5/7] Bugfix to docker --- containers/cat/Dockerfile | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/containers/cat/Dockerfile b/containers/cat/Dockerfile index 5f88d2f..10f400f 100644 --- a/containers/cat/Dockerfile +++ b/containers/cat/Dockerfile @@ -67,6 +67,8 @@ RUN git clone https://github.com/dahlo/WiggleTools RUN conda create -y -n cat python=3.7 \ && echo "conda activate cat" >> ~/.bashrc +SHELL ["/bin/bash", "--login", "-c"] + RUN conda install -n cat -c conda-forge -c bioconda -c defaults -y \ pyfasta luigi seaborn pandas \ ete3 pysam numpy scipy bx-python bcbio-gff biopython parasail-python configobj sqlalchemy \ @@ -77,12 +79,12 @@ RUN conda install -n cat -c conda-forge -c bioconda -c defaults -y \ ucsc-bedsort ucsc-bedtobigbed ucsc-fasize ucsc-wigtobigwig ucsc-hgloadchain RUN conda activate cat \ - && conda install -n cat -y git+https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit.git + && python3 -m pip install -y https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit.git RUN python3 --version RUN conda activate cat \ - python3 --version + && python3 --version RUN mkdir -p /augustus \ && git clone https://github.com/Gaius-Augustus/Augustus.git \ From f8b25f5900f88102d53a786d06d8294138432d00 Mon Sep 17 00:00:00 2001 From: bbimber Date: Sun, 25 Jan 2026 20:19:46 -0800 Subject: [PATCH 6/7] Bugfix to docker --- containers/cat/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/containers/cat/Dockerfile b/containers/cat/Dockerfile index 10f400f..4741bc7 100644 --- a/containers/cat/Dockerfile +++ b/containers/cat/Dockerfile @@ -79,7 +79,7 @@ RUN conda install -n cat -c conda-forge -c bioconda -c defaults -y \ ucsc-bedsort ucsc-bedtobigbed ucsc-fasize ucsc-wigtobigwig ucsc-hgloadchain RUN conda activate cat \ - && python3 -m pip install -y https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit.git + && python3 -m pip install git+https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit.git RUN python3 --version From 59e6707369f522088057bcd560b2149edf8a1f19 Mon Sep 17 00:00:00 2001 From: bbimber Date: Sun, 25 Jan 2026 21:40:45 -0800 Subject: [PATCH 7/7] Bugfix to docker --- containers/cat/Dockerfile | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/containers/cat/Dockerfile b/containers/cat/Dockerfile index 4741bc7..18e4b69 100644 --- a/containers/cat/Dockerfile +++ b/containers/cat/Dockerfile @@ -89,14 +89,19 @@ RUN conda activate cat \ RUN mkdir -p /augustus \ && git clone https://github.com/Gaius-Augustus/Augustus.git \ && cp -r /Augustus/config/ /augustus/config/ \ - && mv Augustus /root/Augustus + && mv Augustus /root/tools/Augustus ENV AUGUSTUS_CONFIG_PATH=/augustus/config/ #COPY --from=builder /augustus/bin/* /bin/ #COPY --from=builder /augustus/scripts/* /bin/ -RUN cd WiggleTools && make \ - && cp /WiggleTools/bin/* /bin/ +RUN wget -O wiggletools.tar.gz https://github.com/Ensembl/WiggleTools/archive/c1daac89e3775bc8f96376fc1ed7f7e645ce168c.tar.gz \ + && tar --strip-components=1 -xzf wiggletools.tar.gz \ + && make LIBS='-lwiggletools -lBigWig -lcurl -lhts -lgsl -lgslcblas -lz -lpthread -lm -llzma' + + +#RUN cd WiggleTools && make \ +# && cp /WiggleTools/bin/* /bin/ SHELL ["conda", "run", "--no-capture-output", "-n", "cat", "/bin/bash", "-c"] \ No newline at end of file