Dependencies

Funannotate has a lot of dependencies. However, it also comes with a few tools to help you get everything installed. The first is that of funannotate check. You’ll see in the output below that the fasta tool is missing, which is Bill Pearsons fasta36 a dependency of the PASA pipeline. Also the $PASAHOME` and $TRINITYHOME` variables are not set, that is because on this particular machine they are not installed, i.e. funannotate will alert you at runtime if it is missing a dependency.

$ funannotate check --show-versions
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Checking dependencies for funannotate v1.4.0
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You are running Python v 2.7.11. Now checking python packages...
biopython: 1.70
goatools: 0.7.11
matplotlib: 2.1.1
natsort: 5.2.0
numpy: 1.12.1
pandas: 0.22.0
psutil: 5.4.3
requests: 2.18.4
scikit-learn: 0.19.0
scipy: 0.19.1
seaborn: 0.8.1
All 11 python packages installed


You are running Perl v 5.026001. Now checking perl modules...
Bio::Perl: 1.007002
Carp: 1.42
Clone: 0.39
DBD::SQLite: 1.56
DBD::mysql: 4.046
DBI: 1.641
DB_File: 1.84
Data::Dumper: 2.167
File::Basename: 2.85
File::Which: 1.22
Getopt::Long: 2.5
Hash::Merge: 0.300
JSON: 2.97001
LWP::UserAgent: 6.33
Logger::Simple: 2.0
POSIX: 1.76
Parallel::ForkManager: 1.19
Pod::Usage: 1.69
Scalar::Util::Numeric: 0.40
Storable: 2.62
Text::Soundex: 3.05
Thread::Queue: 3.12
Tie::File: 1.02
URI::Escape: 3.31
YAML: 1.24
threads: 2.21
threads::shared: 1.58
All 27 Perl modules installed


Checking external dependencies...
RepeatMasker: RepeatMasker 4.0.7
RepeatModeler: RepeatModeler 1.0.11
Trinity: 2.5.1
augustus: 3.2.1
bamtools: bamtools 2.4.0
bedtools: bedtools v2.27.1
blat: BLAT v35
diamond: diamond 0.9.19
emapper.py: emapper-1.0.3
ete3: 3.1.1
exonerate: exonerate 2.4.0
fasta: no way to determine
gmap: 2017-06-20
gmes_petap.pl: 4.30
hisat2: 2.1.0
hmmscan: HMMER 3.1b2 (February 2015)
hmmsearch: HMMER 3.1b2 (February 2015)
java: 1.8.0_92
kallisto: 0.43.1
mafft: v7.313 (2017/Nov/15)
makeblastdb: makeblastdb 2.7.1+
minimap2: 2.10-r761
nucmer: 3.1
pslCDnaFilter: no way to determine
rmblastn: rmblastn 2.2.27+
samtools: samtools 1.8
tRNAscan-SE: 1.23 (April 2002)
tbl2asn: unknown, likely 25.3
tblastn: tblastn 2.7.1+
trimal: trimAl v1.4.rev15 build[2013-12-17]
All 30 external dependencies are installed

Checking Environmental Variables...
$FUNANNOTATE_DB=/usr/local/share/funannotate
$PASAHOME=/Users/jon/software/PASApipeline
$TRINITYHOME=/usr/local/opt/trinity
$EVM_HOME=/Users/jon/software/evidencemodeler
$AUGUSTUS_CONFIG_PATH=/Users/jon/software/augustus/config
$GENEMARK_PATH=/Users/jon/software/gmes_petap
$BAMTOOLS_PATH=/Users/jon/software/bamtools-2.4.0/bin
All 7 environmental variables are set
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