SchwarzEM
commented
6 years ago Details of how I set up HINGE and tried running its demo assembly:
cd /home/schwarz/src ;
rm -rf HINGE_20feb2018 ;
git clone https://github.com/fxia22/HINGE.git HINGE_21feb2018 ;
cd HINGE_21feb2018 ;
git submodule init ;
git submodule update ;
# fix some very bad misspecifications in here so that the thing has a chance to work:
cp -ip ./utils/build.sh ./utils/orig_build.sh_file ;
cat ./utils/build.sh ;[contents of original ./utils/build.sh:]
#!/bin/bash
pwd=$PWD
cd $pwd/thirdparty/DAZZ_DB
make -j 8
cd $pwd/thirdparty//DALIGNER
make -j 8
cd $pwd/thirdparty/DASCRUBBER
make -j 8
cd $pwd/thirdparty/DEXTRACTOR
make -j 8
cd $pwd
mkdir build
cd $pwd/build
cmake .. -DCMAKE_INSTALL_PREFIX=../inst -DCMAKE_C_COMPILER=gcc-4.8 -DCMAKE_CXX_COMPILER=g++-4.8
make -j 8
make install
exit $?pico ./utils/build.sh ;
diff ./utils/orig_build.sh_file ./utils/build.sh ;[output of "diff ./utils/orig_build.sh_file ./utils/build.sh":]
13,14c13,14
< cd $pwd/thirdparty/DEXTRACTOR
< make -j 8
---
> # cd $pwd/thirdparty/DEXTRACTOR
> # make -j 8
19c19
< cmake .. -DCMAKE_INSTALL_PREFIX=../inst -DCMAKE_C_COMPILER=gcc-4.8 -DCMAKE_CXX_COMPILER=g++-4.8
---
> cmake .. -DCMAKE_INSTALL_PREFIX=../inst -DCMAKE_C_COMPILER=gcc-4.9 -DCMAKE_CXX_COMPILER=g++-4.9CPATH="/usr/include/hdf5/serial" ; # $CPATH is empty on my system
export CPATH ;
[check to see that I have everything installed that I need:]
python -m pip install --user pbcore ;
[can't run this: python3 -m pip install --user pbcore ;]
[for all of the others, enforce local pip to both python2 and python3]
python -m pip install --user ujson ;
python3 -m pip install --user ujson ;
python -m pip install --user colormap ;
python3 -m pip install --user colormap ;
python -m pip install --user easydev ;
python3 -m pip install --user easydev ;
python -m pip install --user configparser ;
python3 -m pip install --user configparser ;
[finally, this should work, so run it:]
./utils/build.sh ;
[before I try working with this, make sure this script has a chance of working:]
cd /home/schwarz/src/HINGE_21feb2018/utils ;
cp -ip setup.sh orig_setup.sh_file ;
pico setup.sh ;
[remove DEXTRACTOR from the $PATH, since I didn't compile it; remove racon, since it's not really there any more]
[also, get rid of the $PWD nonsense, which just makes the damn thing fail when invoked from anywhere else]
cat setup.sh ;[contents of revised setup.sh:]
PPWD=/home/schwarz/src/HINGE_21feb2018
export PATH="$PATH:$PPWD/thirdparty:$PPWD/thirdparty/DALIGNER:$PPWD/thirdparty/DAZZ_DB:$PPWD/thirdparty/DASCRUBBER:$PPWD/inst/bin"
export MANPATH="$MANPATH:$PPWD/inst/share/man"cd /home/schwarz/src/HINGE_21feb2018/demo/ecoli_demo ;
cp -ip run.sh orig_run.sh_file ;
[Make wget run silently, and put "source /home/schwarz/src/HINGE_21feb2018/utils/setup.sh ;" in the run.sh script:]
pico run.sh ;
chmod +x run.sh ;
cat run.sh ;[contents of run.sh, edited to have slightly tighter line-command syntax and to emit tracking text files, so that I can stop having to guess when the thing failed:]
#!/bin/bash
# put this *inside* the script so that there is no chance for it not to be invoked:
source /home/schwarz/src/HINGE_21feb2018/utils/setup.sh ;
# use '-q' mode to avoid cluttering up the nohup files:
wget -q http://gembox.cbcb.umd.edu/mhap/raw/ecoli_p4_filtered.fastq.gz ;
gunzip ecoli_p4_filtered.fastq.gz ;
seqtk seq -a ecoli_p4_filtered.fastq > reads.fasta ;
hinge correct-head reads.fasta reads.pb.fasta map.txt ;
echo "hinge correct-head reads.fasta reads.pb.fasta map.txt ;" > step01.txt ;
fasta2DB ecoli reads.pb.fasta ;
echo "fasta2DB ecoli reads.pb.fasta ;" > step02.txt ;
DBsplit ecoli ;
echo "DBsplit ecoli ;" > step03.txt ;
HPC.daligner ecoli | bash -v ;
echo "HPC.daligner ecoli | bash -v ;" > step04.txt ;
rm ecoli.*.ecoli.*.las ;
echo "rm ecoli.*.ecoli.*.las ;" > step05.txt ;
LAmerge ecoli.las ecoli.[0-9].las ;
echo "LAmerge ecoli.las ecoli.[0-9].las ;" > step06.txt ;
DASqv -c100 ecoli ecoli.las ;
echo "DASqv -c100 ecoli ecoli.las ;" > step07.txt ;
mkdir log ;
echo "mkdir log ;" > step08.txt ;
hinge filter --db ecoli --las ecoli --mlas -x ecoli --config ../../utils/nominal.ini ;
echo "hinge filter --db ecoli --las ecoli --mlas -x ecoli --config ../../utils/nominal.ini ;" > step09.txt ;
hinge maximal --db ecoli --las ecoli --mlas -x ecoli --config ../../utils/nominal.ini ;
echo "hinge maximal --db ecoli --las ecoli --mlas -x ecoli --config ../../utils/nominal.ini ;" > step10.txt ;
hinge layout --db ecoli --las ecoli --mlas -x ecoli --config ../../utils/nominal.ini -o ecoli ;
echo "hinge layout --db ecoli --las ecoli --mlas -x ecoli --config ../../utils/nominal.ini -o ecoli ;" > step11.txt ;
hinge clip ecoli.edges.hinges ecoli.hinge.list demo ;
echo "hinge clip ecoli.edges.hinges ecoli.hinge.list demo ;" > step12.txt ;
hinge draft-path $PWD ecoli ecolidemo.G2.graphml ;
echo "hinge draft-path $PWD ecoli ecolidemo.G2.graphml ;" > step13.txt ;
hinge draft --db ecoli --las ecoli --mlas --prefix ecoli --config ../../utils/nominal.ini --out ecoli.draft ;
echo "hinge draft --db ecoli --las ecoli --mlas --prefix ecoli --config ../../utils/nominal.ini --out ecoli.draft ;" > step14.txt ;
hinge correct-head ecoli.draft.fasta ecoli.draft.pb.fasta draft_map.txt ;
echo "hinge correct-head ecoli.draft.fasta ecoli.draft.pb.fasta draft_map.txt ;" > step15.txt ;
fasta2DB draft ecoli.draft.pb.fasta ;
echo "fasta2DB draft ecoli.draft.pb.fasta ;" > step16.txt ;
HPC.daligner ecoli draft | bash -v ;
echo "HPC.daligner ecoli draft | bash -v ;" > step17.txt ;
hinge consensus draft ecoli draft.ecoli.las ecoli.consensus.fasta ../../utils/nominal.ini ;
echo "hinge consensus draft ecoli draft.ecoli.las ecoli.consensus.fasta ../../utils/nominal.ini ;" > step18.txt ;
hinge gfa $PWD ecoli ecoli.consensus.fasta ;
echo "hinge gfa $PWD ecoli ecoli.consensus.fasta ;" > step19.txt ;[try the test data run:]
cd /home/schwarz/src/HINGE_21feb2018/demo/ecoli_demo ;
nohup ./run.sh 1>nohup1.out 2>nohup1.err &
ilanshom
I have tried to compile HINGE and run it on one of its own test instances. The compilation superficially appears to work, but the test instance fails at (or before) the following step:
hinge draft-path $PWD ecoli ecolidemo.G2.graphml ;
To keep from bloating the text of this initial post greatly, I will provide full details of the failure as comments, rather than in the initial post itself.