Running and Verifying SNAP

Run the following command to declare the Cufflinks environment:
```
export PATH=/path/to/CUFFLINKS/build/bin:$PATH
```
Run the following command to process the gtf test case:
```
gffread hg38.gtf -o- >hg38.gff3
```
Run the following command to use Maker to process the gff3 test case:
```
/path/to/MAKER/maker/src/bin/maker2zff hg38.gff3
```
The genome.ann(ZFF) and genome.dna files are generated in the current directory.

Run the following commands to use fathom and forge to process the test cases:

fathom genome.ann genome.dna -categorize 1000
fathom uni.ann uni.dna -export 1000 -plus
forge export.ann export.dna
hmm-assembler.pl test . >test.hmm

Run the following commands to decompress and rename the test cases:

gzip -d GCA_000001405.15_GRCh38_full_analysis_set.fna.gz
mv GCA_000001405.15_GRCh38_full_analysis_set.fna hs38DH.fasta

Run the following command to perform a test:
```
{ time snap test.hmm hs38DH.fasta>snap.zff ; } 2>&1 |tee snap.log
```
If the following information is displayed, the verification is successful:

Parent topic: SNAP 2013-11-29 Porting Guide (CentOS 7.6)