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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