ERROR: gmes_petap.pl not installed ERROR: signalp not installed when they are

[joana-morais]

When installing funannotate via conda I need to add a couple of dependencies, such as signalp and gmes_petap.pl. After doing so and making sure that they are installed, I do funannotate check --show-versions and recieve:

ERROR: gmes_petap.pl not installed ERROR: signalp not installed

OS/Install Information

• output of funannotate check --show-versions
  `-------------------------------------------------------
  Checking dependencies for 1.8.1

---

You are running Python v 3.7.8. Now checking python packages...
biopython: 1.76
goatools: 1.0.11
matplotlib: 3.3.3
natsort: 7.0.1
numpy: 1.19.4
pandas: 1.1.4
psutil: 5.7.0
requests: 2.25.0
scikit-learn: 0.23.2
scipy: 1.5.3
seaborn: 0.11.0
All 11 python packages installed

You are running Perl v b'5.026002'. Now checking perl modules...
Bio::Perl: 1.007002
Carp: 1.38
Clone: 0.42
DBD::SQLite: 1.64
DBD::mysql: 4.046
DBI: 1.642
DB_File: 1.855
Data::Dumper: 2.173
File::Basename: 2.85
File::Which: 1.23
Getopt::Long: 2.5
Hash::Merge: 0.300
JSON: 4.02
LWP::UserAgent: 6.39
Logger::Simple: 2.0
POSIX: 1.76
Parallel::ForkManager: 2.02
Pod::Usage: 1.69
Scalar::Util::Numeric: 0.40
Storable: 3.15
Text::Soundex: 3.05
Thread::Queue: 3.12
Tie::File: 1.02
URI::Escape: 3.31
YAML: 1.29
threads: 2.15
threads::shared: 1.56
All 27 Perl modules installed

Checking Environmental Variables...
$PASAHOME=/home/lebi_kimura/miniconda3/envs/funannotate/opt/pasa-2.4.1
$TRINITY_HOME=/home/lebi_kimura/miniconda3/envs/funannotate/opt/trinity-2.8.5
$EVM_HOME=/home/lebi_kimura/miniconda3/envs/funannotate/opt/evidencemodeler-1.1.1
$AUGUSTUS_CONFIG_PATH=/home/lebi_kimura/miniconda3/envs/funannotate/config/
ERROR: FUNANNOTATE_DB not set. export FUNANNOTATE_DB=/path/to/dir
ERROR: GENEMARK_PATH not set. export GENEMARK_PATH=/path/to/dir

Checking external dependencies...
ERROR: signalp found but error running signalp
PASA: 2.4.1
CodingQuarry: 2.0
Trinity: 2.8.5
augustus: 3.3.3
bamtools: bamtools 2.5.1
bedtools: bedtools v2.29.2
blat: BLAT v36
diamond: 2.0.4
emapper.py: There was an error retrieving eggnog-mapper DB data: not a valid file "/home/lebi_kimura/miniconda3/envs/funannotate/lib/python3.7/site-packages/data/eggnog.db"
Maybe you need to run download_eggnog_data.py
emapper-2.1.12 / Expected eggNOG DB version: 5.0.2 / Installed eggNOG DB version: unknown / Diamond found: diamond 2.0.4 / MMseqs2 found: 113e3212c137d026e297c7540e1fcd039f6812b1 / Compatible novel families DB version: 1.0.1

ete3: 3.1.2
exonerate: exonerate 2.4.0
fasta: no way to determine
glimmerhmm: 3.0.4
gmap: 2017-11-15
hisat2: 2.2.1
hmmscan: HMMER 3.3.1 (Jul 2020)
hmmsearch: HMMER 3.3.1 (Jul 2020)
java: 11.0.8-internal
kallisto: 0.46.1
mafft: v7.471 (2020/Jul/3)
makeblastdb: makeblastdb 2.2.31+
minimap2: 2.17-r941
proteinortho: 6.0.24
pslCDnaFilter: no way to determine
salmon: salmon 0.14.1
samtools: samtools 1.10
snap: 2006-07-28
stringtie: 2.1.4
tRNAscan-SE: 2.0.6 (May 2020)
tantan: tantan 13
tbl2asn: no way to determine, likely 25.X
tblastn: tblastn 2.2.31+
trimal: trimAl v1.4.rev15 build[2013-12-17]
trimmomatic: 0.39
ERROR: gmes_petap.pl not installed
ERROR: signalp not installed
`

How should I fix this?

[nextgenusfs]

Either set the GENEMARK_PATH environmental variable or add the genemark folder to your PATH so that gmes_petap.pl is callable from the funannotate environment. All this script is doing is seeing if these command line tools are in your PATH.