-
Notifications
You must be signed in to change notification settings - Fork 10
/
config.txt
192 lines (162 loc) · 8.49 KB
/
config.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
#base path to pipeline ESSENTIAL
MFLRDir /g/bork3/home/hildebra/dev/Perl/reAssemble2Spec/
globalTmpDir /scratch/bork/hildebra/MATAFILER/
#globalTmpDir /tmp/bork/hildebra/MATAFILER/
nodeTmpDir /tmp/MATAFILER/
qsubPEenv smp
subXtraCmd
## external programs
# programs / DBs ESSENTIAL
samtools [MFLRDir]/bin/samtools
spades /g/bork3/home/hildebra/bin/Spades/SPAdes-3.10.1-Linux/bin/spades.py
megahit /g/bork3/home/hildebra/bin/megahit_v1.1.2_LINUX_CPUONLY_x86_64-bin/megahit
bwt2 [MFLRDir]/bin/bowtie2
bwa /g/bork3/home/hildebra/bin/bwa/./bwa
prodigal [MFLRDir]/bin/prodigal
sambamba [MFLRDir]/bin/sambamba_v0.6.4
pigz [MFLRDir]/bin/pigz
jgiDepth [MFLRDir]/bin/jgi_summarize_bam_contig_depths #/g/bork3/home/hildebra/bin/metabat/./jgi_summarize_bam_contig_depths
bedCov [MFLRDir]/bin/./genomeCoverageBed
FMGdir [MFLRDir]/bin/fetchMG/
hmmsearch [MFLRDir]/bin/hmmsearch
essentialHMM [MFLRDir]/DB/essential.hmm
essentialEUK [MFLRDir]/DB/eukCore.hmm
trimomatic [MFLRDir]/bin/trimmomatic-0.36.jar
illuminaTS3pe [MFLRDir]/DB/TruSeq3-PE.fa
illuminaTS3se [MFLRDir]/DB/TruSeq3-SE.fa
# SNPs / tree building - not public currently
pal2nal perl /g/bork3/home/hildebra/bin/pal2nal.v14/pal2nal.pl
phyml /g/bork3/home/hildebra/bin/ete/ext_apps-latest/bin/phyml
raxml /g/bork3/home/hildebra/bin/RAxML/raxmlHPC-PTHREADS-SSE3
iqtree /g/bork3/home/hildebra/bin/iqtree-1.6.3.a-Linux/bin/iqtree
msaprobs /g/bork3/home/hildebra/bin/MSAProbs-0.9.7/MSAProbs/msaprobs
clustalo /g/bork3/home/hildebra/bin/clustalo/clustalo-1.2.4-Ubuntu-x86_64
fasttree /g/bork3/home/hildebra/bin/fasttree/./FastTreeMP
fasta2phylip_scr perl /g/bork3/home/hildebra/dev/Perl/formating/fasta2phylip.pl
trimal /g/bork3/home/hildebra/bin/trimal/source/trimal
vsearch /g/bork3/home/hildebra/bin/vsearch-2.6.2-linux-x86_64/bin/./vsearch
swipe /g/bork3/home/hildebra/bin/swipe/./swipe
makeblastdb /g/bork5/hildebra/dev/lotus//bin//ncbi-blast-2.2.29+/bin/makeblastdb
# experimental
sinvict /g/bork3/home/hildebra/bin/sinvict/./sinvict
br2dCnt /g/bork3/home/hildebra/bin/bam-readcount/bin/./bam-readcount
seqtk /g/bork3/home/hildebra/bin/seqtk/seqtk
bam2cns /g/bork3/home/hildebra/bin/proovread/bin/bam2cns
treeDistScr perl /g/bork3/home/hildebra/dev/Perl/reAssemble2Spec/bin/distv9.pl
fna2faa /g/bork3/home/hildebra/dev/Perl/reAssemble2Spec/bin/fna2faa
# scaffolding operations (imrpoving assemblies with mate pairs)
nxtrim /g/bork3/home/hildebra/bin/NxTrim/./nxtrim
BESST /g/bork3/home/hildebra/bin/BESST/./runBESST
gapfiller perl /g/bork3/home/hildebra/bin/GapFiller/GapFiller_n.pl
# gene catalogue
cdhit [MFLRDir]/bin/cd-hit
# miTag related
#lambda [MFLRDir]/bin/lambda2-1.9.4-Linux-x86_64/bin/./lambda2
lambda [MFLRDir]/bin/./lambda
lambdaIdx [MFLRDir]/bin/lambda_indexer
#requires version 2.0 with databases in "srtMRNA_path/rRNA_databases/silva*"
srtMRNA_path /g/bork3/home/hildebra/bin/sortmerna-2.0/
srtMRNA_DBs silva-euk-18s-id95.fasta,silva-bac-16s-id90.fasta,silva-arc-16s-id95.fasta,silva-euk-28s-id98.fasta,silva-bac-23s-id98.fasta,silva-arc-23s-id98.fasta
mergeRdScr [MFLRDir]/bin/merge-paired-reads.sh
unmergeRdScr [MFLRDir]/bin/unmerge-paired-reads.sh
LSUdbFA /g/bork3/home/hildebra/DB/MarkerG/SILVA/128//SLV_128_LSU.fasta
LSUtax /g/bork3/home/hildebra/DB/MarkerG/SILVA/128/SLV_128_LSU.tax
SSUdbFA /g/bork3/home/hildebra/DB/MarkerG/SILVA/128/SLV_128_SSU.fasta
SSUtax /g/bork3/home/hildebra/DB/MarkerG/SILVA/128/SLV_128_SSU.tax
ITSdbFA /g/bork3/home/hildebra/DB/MarkerG/ITS_combi/ITS_comb.fa
ITStax /g/bork3/home/hildebra/DB/MarkerG/ITS_combi/ITS_comb.tax
PR2dbFA /g/bork3/home/hildebra/DB/MarkerG/PR2//gb203_pr2_all_10_28_99p.fasta
PR2tax /g/bork3/home/hildebra/DB/MarkerG/PR2//PR2_taxonomy.txt
#only if euk metagenomes to be processed
augustus /g/bork3/home/hildebra/bin/augustus-3.2.1/bin/augustus
#very specific usage, mostly not required
d2meta /g/bork3/home/hildebra/bin/d2Meta/d2Meta/d2Meta.out
nonpareil /g/bork3/home/hildebra/bin/nonpareil/nonpareil #estimate metag coverage sequenced in your samples
hmmer3 /g/bork3/home/hildebra/bin/hmmer-3.0/hmm30/bin/hmmsearch #FOAM KEGG assignments gene cat
mmseqs2 /g/bork3/home/hildebra/bin/mmseqs2/bin/mmseqs #experimental clustering of genes
growthP python /g/bork3/home/hildebra/bin/growthpred-v1.07/./growthpred-v1.07.py
rnammer /g/bork3/home/hildebra/bin/rna_mmer/./rnammer
#no longer used
#usearch /g/bork3/home/hildebra/bin/usearch/usearch8.0.1421M_i86linux32_fh
#novosrt /g/bork3/home/hildebra/bin/novocraft/novosort
blat /g/bork3/home/hildebra/bin/blat/./blat
nucmer /g/bork3/home/hildebra/bin/MUMmer3.23/./nucmer
#taxonomic profiling, if requrested
metPhl2 /g/bork3/home/hildebra/bin/metaphlan2/metaphlan2.py
metPhl2Merge /g/bork3/home/hildebra/bin/metaphlan2/utils/merge_metaphlan_tables.py
kraken /g/scb/bork/hildebra/DB/kraken/./kraken
motu2_dir /g/bork3/home/hildebra/bin/mOTUs_v2/
kaijuDir /g/bork3/home/hildebra/bin/kaiju/bin/
microCens python /g/bork3/home/hildebra/bin/MicrobeCensus-1.1.0/scripts/run_microbe_census.py
#functional profiling
diamond [MFLRDir]/bin/./diamond
emapper python /g/bork3/home/hildebra/bin/eggnog-mapper/emapper.py
mp3 /g/bork3/home/hildebra/bin/mp3v1.0/
#if read merge is attempted in any step (typically for miTag, profiling)
flash [MFLRDir]/bin/flash
#microsats
mreps [MFLRDir]/bin/mreps
#binning
kmerFreqs perl [MFLRDir]/bin/calc.kmerfreq.pl
maxBinFrmt perl [MFLRDir]/secScripts/maxBin_rewrk.pl
maxBin perl [MFLRDir]/bin/MaxBin-1.4.2/run_MaxBin.pl
#my own C++ progs ESSENTIAL
rare [MFLRDir]/bin/rtk
sdm [MFLRDir]/bin/sdm
LCA [MFLRDir]/bin/./LCA
readCov [MFLRDir]/bin/./rdCover
#local scripts ESSENTIAL
cLSUSSU_scr perl [MFLRDir]/miTag/catchLSUSSU.pl
lotusLCA_cLSU_scr [MFLRDir]/miTag/lotus_LCA_blast3.pl
krakCnts_scr [MFLRDir]/secScripts/krak_count_tax.pl
genelength_scr [MFLRDir]/secScripts/geneLengthFasta.pl
secCogBin_scr [MFLRDir]/secScripts/parseBlastFunct2.pl
KrisABR_scr perl [MFLRDir]/secScripts/ABRblastFilter2.pl
sepCts_scr perl [MFLRDir]/secScripts/separateContigs.pl
assStat_scr perl [MFLRDir]/secScripts/assemblathon_stats.pl
renameCtg_scr [MFLRDir]/secScripts/renameCtgs.pl
sizFilt_scr perl [MFLRDir]/secScripts/sizeFilterFas.pl
buildTree_scr perl [MFLRDir]/helpers/buildTree4.pl
sizSplit_scr [MFLRDir]/secScripts/splitFNAbyLength.pl
contigKgdSplit_scr [MFLRDir]/secScripts/sortCtgKingdom.pl
calcGC_scr [MFLRDir]/secScripts/calcGC.pl
sortSepReLen_scr [MFLRDir]/secScripts/sepReadLength.pl
secCogBin_scr [MFLRDir]/secScripts/parseBlastFunct.pl
extre100_scr [MFLRDir]/helpers/extrAllE100GC.pl
decoyDB_scr [MFLRDir]/secScripts/./deployMapDB.pl
bamHdFilt_scr [MFLRDir]/secScripts/./correctBamHD.pl
hmmBestHit_scr [MFLRDir]/secScripts/bmn-HMMerBestHit.py
mrgDia_scr [MFLRDir]/helpers/./combine_DIA.pl
mrgMiTag_scr [MFLRDir]/secScripts/miTagTaxTable.pl
cmpBinScr [MFLRDir]/secScripts/compoundBinning.pl
FMGrwk_scr perl [MFLRDir]/secScripts/FMG_rwk.pl
growth_scr perl [MFLRDir]/helpers/growthRate.pl
consCntupVCF_scr perl /g/bork3/home/hildebra/dev/Perl/reAssemble2Spec/helpers/SNP/consFNA2vcf.pl
mp3Prs perl [MFLRDir]/secScripts/parseMP3.pl
unsplitKrak_scr perl [MFLRDir]/secScripts/unsplit_krak.pl
specIGC_scr perl [MFLRDir]/helpers/GC/annotateMGwSpecIs.pl
#options for filters etc ESSENTIAL
#baseSDMopt_rel [MFLRDir]/data/sdm_opt_inifilter_relaxed_noProb.txt
baseSDMopt_rel [MFLRDir]/data/sdm_opt_inifilter_relaxed.txt
baseSDMopt [MFLRDir]/data/sdm_opt_inifilter.txt
baseSDMoptMiSeq [MFLRDir]/data/sdm_opt_miSeq.txt
baseSDMoptMiSeq_rel [MFLRDir]/data/sdm_opt_miSeq_relaxed.txt
#Databases note that these will be mostly copied to scratch dir, but since indexes are created calc to have at least twice the HD space available for these
#most databases are only required for direct mapping and/or gene catalog assignments
FOAMhmm_DB /g/bork3/home/hildebra/DB/FUNCT/FOAM/FOAM-hmm_rel1.hmm
eggNOG_DB /g/bork3/home/hildebra/DB/FUNCT/eggNOG10/eggnog4.proteins.all.fa
ABresHMM_DB /g/bork/forslund/morehmms/Resfams.hmm
#eggNOG40_path_DB /g/bork3/home/hildebra/DB/FUNCT/eggNOG10/
eggNOG40_path_DB /g/bork3/home/hildebra/DB/FUNCT/eggNOGmapper/
Moh_path_DB /g/bork3/home/hildebra/DB/FUNCT/MohFuncts/
CAZy_path_DB /g/bork3/home/hildebra/DB/FUNCT/CAZy/
ABRfors_path_DB /g/bork3/home/hildebra/DB/FUNCT/ABR_FORS/
ABRcard_path_DB /g/bork3/home/hildebra/DB/FUNCT/ABR_Card/
KEGG_path_DB /g/bork3/home/hildebra/DB/FUNCT/KEGG/
ACL_path_DB /g/bork3/home/hildebra/DB/FUNCT/Aclame/
TCDB_path_DB /g/bork3/home/hildebra/DB/FUNCT/TCDB/
PATRIC_VIR_path_DB /g/bork3/home/hildebra/DB/FUNCT/PATRIC/VirFac_KF/
ABprod_path_DB /g/bork3/home/hildebra/DB/FUNCT/ABprod_v1/
VirDB_path_DB /g/bork3/home/hildebra/DB/FUNCT/VIRDB/
Kraken_path_DB /g/scb/bork/hildebra/DB/kraken/
Kaiju_path_DB /g/scb/bork/hildebra/DB/kaiju/