Commit db4e046a authored by Glenn Hickey's avatar Glenn Hickey
Browse files

update minigraph to fix weird gcc7.5 crash

parent 4047f06e
Pipeline #1521 failed with stage
in 80 minutes and 32 seconds
......@@ -59,7 +59,7 @@ fi
cd ${pangenomeBuildDir}
git clone https://github.com/lh3/minigraph.git
pushd minigraph
git checkout c012ee420c1d498f6d53453ece8ed7e7e7d487a1
git checkout 45d11e42498130fdd45b7c19a7ec285ce09cfece
# hack in flags support
sed -i Makefile -e 's/CFLAGS=/CFLAGS+=/'
make -j ${numcpu}
......
......@@ -461,7 +461,7 @@ This command will create a vg and hal file for each chromosome in ${MYBUCKET}/al
```
aws s3 cp ${MYBUCKET}/chroms-hprc-${VERSION}-mc-grch38/chromfile.txt .
cactus-align-batch ${MYJOBSTORE} ./chromfile.txt ${MYBUCKET}/align-hprc-${VERSION}-mc-grch38 --alignCores 16 --realTimeLogging --alignOptions "--pangenome --pafInput --maxLen 10000 --reference GRCh38 --realTimeLogging --outVG" --batchSystem mesos --provisioner aws --defaultPreemptable --nodeType r5.8xlarge:1.5 --nodeStorage 1000 --maxNodes 10 --betaInertia 0 --targetTime 1 --configFile config_align.xml --logFile hprc-${VERSION}-mc-grch38.align.log
cactus-align-batch ${MYJOBSTORE} ./chromfile.txt ${MYBUCKET}/align-hprc-${VERSION}-mc-grch38 --alignCores 16 --realTimeLogging --alignOptions "--pangenome --pafInput --maxLen 10000 --reference GRCh38 --realTimeLogging --outVG" --batchSystem mesos --provisioner aws --defaultPreemptable --nodeType r5.8xlarge:1.5 --nodeStorage 1000 --maxNodes 10 --betaInertia 0 --targetTime 1 --logFile hprc-${VERSION}-mc-grch38.align.log
```
### HPRC Graph: Creating the Whole-Genome Graph
......@@ -485,7 +485,7 @@ We also use the `--giraffe --vcf` options to create the Giraffe indexes and VCF.
We use as input the vg files created by the previous call of `graphmap-join` as well as the `--preserveIDs` option to ensure that our new graph is ID-compatible with the full graph.
```
cactus-graphmap-join ${MYJOBSTORE} --vg $(for j in $(for i in `seq 22`; do echo chr$i; done ; echo "chrX chrY chrM chrOther"); do echo ${MYBUCKET}/clip-hprc-${VERSION}-mc-grch38-full/${j}.vg; done) --outDir ${MYBUCKET}/ --outName hprc-${VERSION}-mc-grch38 --reference GRCh38 --wlineSep "." --clipLength 10000 --clipNonMinigraph --vcf --giraffe --preserveIDs --batchSystem mesos --provisioner aws --defaultPreemptable --nodeType r5.8xlarge --nodeStorage 1000 --maxNodes 2 --indexCores 32 --realTimeLogging --logFile hprc-${VERSION}-mc-grch38.join.log
cactus-graphmap-join ${MYJOBSTORE} --vg $(for j in $(for i in `seq 22`; do echo chr$i; done ; echo "chrX chrY chrM chrOther"); do echo ${MYBUCKET}/clip-hprc-${VERSION}-mc-grch38-full/${j}.vg; done) --outDir ${MYBUCKET}/ --outName hprc-${VERSION}-mc-grch38 --reference GRCh38 --wlineSep "." --clipLength 10000 --clipNonMinigraph --vcf --giraffe --preserveIDs --batchSystem mesos --provisioner aws --defaultPreemptable --nodeType r5.16xlarge --nodeStorage 1000 --maxNodes 2 --indexCores 64 --realTimeLogging --logFile hprc-${VERSION}-mc-grch38.join.log
```
**All sequences clipped out by `cactus-graphmap-join` will be saved in BED files in its output directory.**
......
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