Tutorial:TAPIS installation and usage

Question

[JC]

1. download gmap and install cd ~/software

wget http://research-pub.gene.com/gmap/src/gmap-gsnap-2023-07-20.tar.gz

tar xvzf gmap-gsnap-2023-07-20.tar.gz

cd ~/software/gmap-gsnap-2023-07-20

./configure --prefix=$HOME/jcbu/software/gmap

make -j 20

make check

make install

1. build gmap index

cd /home/jcbu/refGenome/gencode/mouse/GRCm38.p6_releaseM20/Sequence/gmapIndex

nohup /home/jcbu/jcbu/software/gmap/bin/gmap_build -d GRCm38.gmap -D

/home/jcbu/refGenome/gencode/mouse/GRCm38.p6_releaseM20/Sequence/gmapIndex \

/home/jcbu/refGenome/gencode/mouse/GRCm38.p6_releaseM20/Sequence/WholeGenomeFasta/GRCm38.p6.genome.fa &

3.alignPacBio.py

cd /home/jcbu/YJ/PAIsoseq/ES/TAPIS/gmap/

nohup /usr/bin/python2 /home/jcbu/YJ/PAIsoseq/comp_bio-tapis-44cc05ebc78c/scripts/alignPacBio.m.py \

-p 20 -o Gm_Ctrl_rep1.alignPacBio \

/home/jcbu/refGenome/gencode/mouse/GRCm38.p6_releaseM20/Sequence/gmapIndex/GRCm38.gmap \

GRCm38.gmap \

/home/jcbu/refGenome/gencode/mouse/GRCm38.p6_releaseM20/Sequence/WholeGenomeFasta/GRCm38.p6.genome.fa \

/home/jcbu/YJ/PAIsoseq/ES/ccs/Gm_Ctrl_rep1.bc1001.rmAmbiguous.fasta \

Gm_Ctrl_rep1.alignPacBio.log &

4.run_tapis.py

cd /home/jcbu/YJ/PAIsoseq/ES/TAPIS/gmap/

nohup /usr/bin/python2 /home/jcbu/YJ/PAIsoseq/comp_bio-tapis-44cc05ebc78c/scripts/run_tapis.py \

-s 5 \

-p \

-o /home/jcbu/YJ/PAIsoseq/ES/TAPIS/gmap/Gm_Ctrl_rep1.tapis_out \

/home/jcbu/refGenome/gencode/mouse/GRCm38.p6_releaseM20/Annotation/gencode.vM20.annotation.gtf \

/home/jcbu/YJ/PAIsoseq/ES/TAPIS/gmap/Gm_Ctrl_rep1.alignPacBio/aligned.bam \

Gm_Ctrl_rep1.tapis_out.log &

[ATpoint]

Appreciate the contribution but in its current state it's barely useful. Please put formatting. Make an introduction sentence. Explain what the commands are and why you use them. Make it generic. No machine-specific paths and thread/core values. Never use nohup productively.