Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

update wfmash/smoothxg/odgi #371

Merged
merged 3 commits into from
Jan 31, 2024
Merged

update wfmash/smoothxg/odgi #371

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
980069a
update wfmash
AndreaGuarracino Jan 31, 2024
bf686f2
update odgi and smoothxg
AndreaGuarracino Jan 31, 2024
c1fbd6f
odgi stats -sgdl
AndreaGuarracino Jan 31, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions Dockerfile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ RUN apt-get update \
RUN git clone --recursive https://github.com/waveygang/wfmash \
&& cd wfmash \
&& git pull \
&& git checkout 0b191bb84ffdfd257354c1aa82a7f1e13dc536d0 \
&& git checkout e7850f9e9ba743a350b36b5e51ae8c414fba717d \
&& 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) \
Expand All @@ -72,7 +72,7 @@ RUN git clone --recursive https://github.com/ekg/seqwish \
RUN git clone --recursive https://github.com/pangenome/smoothxg \
&& cd smoothxg \
&& git pull \
&& git checkout 9970e0df187c5e1234ace61243f30ddccbbbbdd8 \
&& git checkout ea362342bc4301f767727467953bafcaf147172b \
&& 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 \
Expand Down
6 changes: 3 additions & 3 deletions pggb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -684,12 +684,12 @@ fi

if [[ $do_stats == true ]]; then
$timer -f "$fmt" odgi build -t $threads -P -g "$prefix_seqwish".seqwish.gfa -o "$prefix_seqwish".seqwish.og 2> >(tee -a "$log_file")
odgi stats -i "$prefix_seqwish".seqwish.og -m > "$prefix_seqwish".seqwish.og.stats.yaml 2>&1 | tee -a "$log_file"
odgi stats -i "$prefix_smoothed_output".final.og -m > "$prefix_smoothed_output".final.og.stats.yaml 2>&1 | tee -a "$log_file"
odgi stats -i "$prefix_seqwish".seqwish.og -m -sgdl > "$prefix_seqwish".seqwish.og.stats.yaml 2>&1 | tee -a "$log_file"
odgi stats -i "$prefix_smoothed_output".final.og -m -sgdl > "$prefix_smoothed_output".final.og.stats.yaml 2>&1 | tee -a "$log_file"
if [[ $consensus_spec != false ]]; then
for consensus_graph in "$prefix_smoothed_output"*.cons*.gfa; do
odgi build -t $threads -P -g "$consensus_graph" -o "$consensus_graph".og 2> >(tee -a "$log_file")
odgi stats -i "$consensus_graph".og -m >"$consensus_graph".og.stats.yaml 2>&1 | tee -a "$log_file"
odgi stats -i "$consensus_graph".og -m -sgdl >"$consensus_graph".og.stats.yaml 2>&1 | tee -a "$log_file"
done
fi
fi
Expand Down
Loading