update wfmash/seqwish/smoothxg/odgi

pangenome · Apr 7, 2024 · 35dbe70 · 35dbe70
1 parent 020b609
commit 35dbe70
Show file tree

Hide file tree

Showing 2 changed files with 10 additions and 6 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -32,7 +32,6 @@ RUN apt-get update \
                        curl \
                        pigz \
                        tabix \
-                       bcftools \
                        samtools \
                        wget \
                        pip \
@@ -43,10 +42,15 @@ RUN apt-get update \
     && apt-get purge  \
     && rm -rf /var/lib/apt/lists/*
 
+# current bcftools
+RUN wget https://github.com/samtools/bcftools/releases/download/1.19/bcftools-1.19.tar.bz2 \
+    && tar xjf bcftools-1.19.tar.bz2 \
+    && cd bcftools-1.19/ && ./configure --prefix=/usr/local/bin/ && make && make install && export PATH=/usr/local/bin/bin:$PATH && cd .. && cp /usr/local/bin/bin/* /usr/local/bin/
+
 RUN git clone --recursive https://github.com/waveygang/wfmash \
     && cd wfmash \
     && git pull \
-    && git checkout 7205bf7d693fbbf881d5ad76c3abb34a4df33a2f \
+    && git checkout d7b696087f634f25e4b3de7dd521e1c4bfa3cf0e \
     && git submodule update --init --recursive \
     && sed -i 's/-march=native/-march=sandybridge/g' src/common/wflign/deps/WFA2-lib/Makefile \
     && cmake -H. -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS='-march=sandybridge -Ofast' -Bbuild && cmake --build build -- -j $(nproc) \
@@ -62,7 +66,7 @@ RUN git clone --recursive https://github.com/waveygang/wfmash \
 RUN git clone --recursive https://github.com/ekg/seqwish \
     && cd seqwish \
     && git pull \
-    && git checkout f44b402f0c2e02988d431d9b2e5eba9727cf93a9 \
+    && git checkout 75e807c7e3e92c84068cd3c2c7394eb313732a0a \
     && git submodule update --init --recursive \
     && cmake -H. -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS='-march=sandybridge -Ofast' -Bbuild && cmake --build build -- -j $(nproc) \
     && cp bin/seqwish /usr/local/bin/seqwish \
@@ -72,7 +76,7 @@ RUN git clone --recursive https://github.com/ekg/seqwish \
 RUN git clone --recursive https://github.com/pangenome/smoothxg \
     && cd smoothxg \
     && git pull \
-    && git checkout ea362342bc4301f767727467953bafcaf147172b \
+    && git checkout c216a84c51e8fa462aa0e26e56f08e4580d5c69c \
     && git submodule update --init --recursive \
     && sed -i 's/-msse4.1/-march=sandybridge -Ofast/g' deps/spoa/CMakeLists.txt \
     && sed -i 's/-march=native/-march=sandybridge -Ofast/g' deps/spoa/CMakeLists.txt \
@@ -97,7 +101,7 @@ RUN git clone https://github.com/marschall-lab/GFAffix.git \
     && cd ../ \
     && rm -rf GFAffix
 
-RUN pip install multiqc==1.18
+RUN pip install multiqc==1.21
 
 RUN wget https://github.com/vgteam/vg/releases/download/v1.40.0/vg && chmod +x vg && mv vg /usr/local/bin/vg
 

diff --git a/pggb b/pggb
@@ -670,7 +670,7 @@ if [[ $vcf_spec != false ]]; then
         if [[ ! -s $vcf || $resume == false ]]; then
           echo "[vg::deconstruct] making VCF with reference=$ref and delim=# xxxxxxxxxxxxx $s ------------ $pop_length"
           ( TEMPDIR=$(pwd) $timer -f "$fmt" vg deconstruct -P "$ref" \
-                   -e -a -t $threads "$prefix_smoothed_output".final.gfa >"$vcf" ) 2> >(tee -a "$log_file")
+                   -H "#" -e -a -t $threads "$prefix_smoothed_output".final.gfa >"$vcf" ) 2> >(tee -a "$log_file")
           bcftools stats "$vcf" > "$vcf".stats
         fi