-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathconfig.yaml
105 lines (101 loc) · 9.32 KB
/
config.yaml
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
pfam_db: /ebio/abt2_projects/ag-swart-loxodes/db/pfam/Pfam-A.hmm
assem:
N10 : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.N10.Trinity.fasta"
N26 : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.N26.Trinity.fasta"
N27 : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.N27.Trinity.fasta"
N34 : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.N34.Trinity.fasta"
N38 : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.N38.Trinity.fasta"
N39 : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.N39.Trinity.fasta"
N4 : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.N4.Trinity.fasta"
N44 : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.N44.Trinity.fasta"
N5 : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.N5.Trinity.fasta"
N6 : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.N6.Trinity.fasta"
N70 : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.N70.Trinity.fasta"
N72 : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.N72.Trinity.fasta"
anig_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.anig_yy.Trinity.fasta"
bame2_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.bame2_yy.Trinity.fasta"
bame_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.bame_yy.Trinity.fasta"
cx01_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.cx01_yy.Trinity.fasta"
gacu_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.gacu_yy.Trinity.fasta"
gl04_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.gl04_yy.Trinity.fasta"
gsin2_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.gsin2_yy.Trinity.fasta"
gsin_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.gsin_yy.Trinity.fasta"
kn01_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.kn01_yy.Trinity.fasta"
lstr2_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.lstr2_yy.Trinity.fasta"
lstr_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.lstr_yy.Trinity.fasta"
lx11_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.lx11_yy.Trinity.fasta"
lx13_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.lx13_yy.Trinity.fasta"
rema_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.rema_yy.Trinity.fasta"
sroe_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.sroe_yy.Trinity.fasta"
tc01_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.tc01_yy.Trinity.fasta"
trac_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.trac_yy.Trinity.fasta"
s4111_ksd: "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.s4111_ksd.Trinity.fasta"
s4110_ksd: "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.s4110_ksd.Trinity.fasta"
sa331_kh : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.sa331_kh.Trinity.fasta"
cmag_mm : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.cmag_mm.Trinity.fasta"
pard_mm : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.pard_mm.Trinity.fasta"
sa332_kh : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.sa332_kh.Trinity.fasta"
s4112_ksd : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.s4112_ksd.Trinity.fasta"
bjap_mm : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.bjap_mm.Trinity.fasta"
spol_upp : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.spol_upp.Trinity.fasta"
bsp_mk : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity_se.bsp_mk.Trinity.fasta"
smin_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.smin_yy.Trinity.fasta"
fsal_mm : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.fsal_mm.Trinity.fasta"
cl01_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.cl01_yy.Trinity.fasta"
cvir_mm : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.cvir_mm.Trinity.fasta"
cvir_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.cvir_yy.Trinity.fasta"
polyA_N10 : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.N10.polyA_min7.fasta"
polyA_N26 : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.N26.polyA_min7.fasta"
polyA_N27 : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.N27.polyA_min7.fasta"
polyA_N34 : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.N34.polyA_min7.fasta"
polyA_N38 : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.N38.polyA_min7.fasta"
polyA_N39 : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.N39.polyA_min7.fasta"
polyA_N4 : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.N4.polyA_min7.fasta"
polyA_N44 : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.N44.polyA_min7.fasta"
polyA_N5 : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.N5.polyA_min7.fasta"
polyA_N6 : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.N6.polyA_min7.fasta"
polyA_N70 : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.N70.polyA_min7.fasta"
polyA_N72 : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.N72.polyA_min7.fasta"
polyA_anig_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.anig_yy.polyA_min7.fasta"
# polyA_bame2_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.bame2_yy.polyA_min7.fasta" # too few sequences to be meaningful
polyA_bame_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.bame_yy.polyA_min7.fasta"
polyA_cx01_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.cx01_yy.polyA_min7.fasta"
polyA_gacu_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.gacu_yy.polyA_min7.fasta"
polyA_gl04_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.gl04_yy.polyA_min7.fasta"
polyA_gsin2_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.gsin2_yy.polyA_min7.fasta"
polyA_gsin_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.gsin_yy.polyA_min7.fasta"
polyA_kn01_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.kn01_yy.polyA_min7.fasta"
polyA_lstr2_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.lstr2_yy.polyA_min7.fasta"
polyA_lstr_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.lstr_yy.polyA_min7.fasta"
polyA_lx11_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.lx11_yy.polyA_min7.fasta"
polyA_lx13_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.lx13_yy.polyA_min7.fasta"
polyA_rema_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.rema_yy.polyA_min7.fasta"
# polyA_sroe_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.sroe_yy.polyA_min7.fasta" # too few sequences
polyA_tc01_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.tc01_yy.polyA_min7.fasta"
polyA_trac_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.trac_yy.polyA_min7.fasta"
polyA_smin_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.smin_yy.polyA_min7.fasta"
polyA_cl01_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.cl01_yy.polyA_min7.fasta"
polyA_cvir_yy : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.cvir_yy.polyA_min7.fasta"
polyA_s4110_ksd: "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.s4110_ksd.polyA_min7.fasta"
polyA_s4111_ksd: "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.s4111_ksd.polyA_min7.fasta"
polyA_s4112_ksd: "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.s4112_ksd.polyA_min7.fasta"
polyA_sa331_kh : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.sa331_kh.polyA_min7.fasta"
polyA_sa332_kh : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.sa332_kh.polyA_min7.fasta"
polyA_cmag_mm : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.cmag_mm.polyA_min7.fasta"
polyA_pard_mm : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.pard_mm.polyA_min7.fasta"
polyA_bjap_mm : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.bjap_mm.polyA_min7.fasta"
polyA_fsal_mm : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.fsal_mm.polyA_min7.fasta"
polyA_cvir_mm : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.cvir_mm.polyA_min7.fasta"
polyA_spol_upp : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.spol_upp.polyA_min7.fasta"
polyA_bsp_mk : "/ebio/abt2_projects/ag-swart-karyocode/assembly/trinity.bsp_mk.polyA_min7.fasta"
# Stentor coeruleus - transcriptome assembly not available, using CDS sequences from ciliate.org instead
# http://stentor.ciliate.org/system/downloads/S_coeruleus_Nov2016_CDS.fasta
scoe_cds_ms : "/ebio/abt2_projects/ag-swart-karyocode/db/S_coeruleus_Nov2016_CDS.fasta"
# Blepharisma - use CDS from gene preds instead of assembling transcriptome de novo
bsto_cds_ms : "/ebio/abt2_projects/ag-swart-blepharisma-raw/production/B_stoltei_ATCC/MAC/gene_prediction_v2.0/Bsto_ATCC_MAC_cleaned.0.2.final.CDS.fa"
# Tetrahymena thermophila
# http://www.ciliate.org/system/downloads/3-upd-cds-fasta-2021.fasta
tthe_cds : "/ebio/abt2_projects/ag-swart-karyocode/db/3-upd-cds-fasta-2021.fasta"
# Paramecium tetraurelia
# https://paramecium.i2bc.paris-saclay.fr/files/Paramecium/tetraurelia/51/annotations/ptetraurelia_mac_51/ptetraurelia_mac_51_annotation_v2.0.transcript.fa
ptet_cds : "/ebio/abt2_projects/ag-swart-karyocode/db/ptetraurelia_mac_51_annotation_v2.0.transcript.fa"