r2dt-bio · AntonPetrov · Feb 2, 2025 · Nov 15, 2024 · Nov 15, 2024 · Nov 15, 2024
diff --git a/.dockerignore b/.dockerignore
@@ -9,4 +9,5 @@ docs/_*
 .vscode
 .git
 1.4/
+2.0/
 .venv/
diff --git a/.github/workflows/base-image.yml b/.github/workflows/base-image.yml
diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-ARG BASE_IMAGE_VERSION=v2.0.1
+ARG BASE_IMAGE_VERSION=v2.1
 
 FROM rnacentral/r2dt-base:${BASE_IMAGE_VERSION}
 

diff --git a/Readme.md b/Readme.md
@@ -1,6 +1,6 @@
 # R2DT
 
-**Version 2.0 (2024)**
+**Version 2.1 (2025)**
 
 **[See the R2DT documentation](https://r2dt.readthedocs.io/)** or read the [latest preprint](https://www.biorxiv.org/content/10.1101/2024.09.29.611006v1).
 

diff --git a/base_image/Dockerfile b/base_image/Dockerfile
@@ -2,7 +2,7 @@
 
 ENV tRNAscan_VER=2.0.11 \
     BioEasel_COMMIT=a52f0f7f7cae879bb95489bb794c04c1a0110aa7 \
-    traveler_COMMIT=8054f5bee8327bb158385893e0633d4242676f95 \
+    traveler_COMMIT=78c1cd63dcf40be83d97d07b8eb9eb6a9dc63f7f \
     jiffy_COMMIT=31d6c3b826d432a30620507830749cee58e15e68 \
     Rscape_VER=v2.0.4.c \
     Ribovore_COMMIT=5df943c6f2866d7979bb13c948ca9d8531076898 \
@@ -154,7 +154,7 @@
    VECPLUSDIR="$RIBOINSTALLDIR/vecscreen_plus_taxonomy" \
    RRNASENSORDIR="$RIBOINSTALLDIR/rRNA_sensor"

 ENV \
    RIBOSCRIPTSDIR="$RIBOINSTALLDIR/ribovore" \
    RIBOINFERNALDIR="$RIBOINSTALLDIR/infernal/binaries" \
    RIBOEASELDIR="$RIBOINSTALLDIR/infernal/binaries" \
@@ -165,7 +165,7 @@
    PERL5LIB="$RIBOSCRIPTSDIR":"$RIBOSEQUIPDIR":"$VECPLUSDIR":"$PERL5LIB" \
    PATH="$RIBOSCRIPTSDIR":"$RRNASENSORDIR":"$PATH"

 ENV \
    PATH="$RIBOSCRIPTSDIR":"$RRNASENSORDIR":"$PATH" \
    PATH="$RNA/traveler/bin:$RIBODIR:$RIBOEASELDIR:$RIBOINFERNALDIR:/rna/rscape/bin:/rna/jiffy-infernal-hmmer-scripts:/rna/r2dt:/rna/RNAstructure/exe:$PATH" \
    PERL5LIB="$RIBOSCRIPTSDIR:$RIBOSEQUIPDIR:$VECPLUSDIR:$BIOEASELDIR:$RIBODIR:$EPNOPTDIR:$EPNOFILEDIR:$EPNTESTDIR:$PERL5LIB:/usr/lib/tRNAscan-SE"

diff --git a/data/models.json b/data/models.json
diff --git a/data/tmrna/cm/all.cm b/data/tmrna/cm/all.cm
diff --git a/data/tmrna/cm/all.fa b/data/tmrna/cm/all.fa
@@ -0,0 +1,42 @@
+>tmRNA
+GGGGGUGAACUGGUUUCGACGGGAAUGUUGAUUCCAAAAGCUGCAUGCCGAGGUUGCCGG
+UGACCUCGUAAAACAACCGGCAAAAAAAUAAAUGCCAACAAUAAUUACUAUCGCUCUCGC
+UGCUUAAUAAGCAGCGAGCCGUCCCCCCAGCCCUUGCCUGUUGGGCUGGGAAGGGGCGUC
+AUAAAAGCGGGAUAGCCUUUAGGUUUGCCUGGGGCCUAAAGGCGAAAAUUAAAGAGGCUA
+GCCUUAAGGAAGCCUGUCUGUUGGCAUCCUUAAGGCGAAAAUAAAAAACAGACUAAGCAU
+GUAGAAGCUUUUGGAAUAACAUUUUCGGACGCGGGUUCGAUUCCCGCCACCUCCACCA
+>tmRNA_intron
+GGGGGUGAAUGGUUUCGACGGGGGGCCCUAGCGCCAAGGUUGCAUGCCGAGGAUGCCGGC
+GACCUCGUUAAAAAGCCGGCAAAAAUAUAAAUGCCAACAAUAAUAACUACGCUUUCGCUG
+CUUAAUGCAGCGAAGACGUCCUCCCCCUCCUCGCCUGAUGGAGGGGGAAAGGGCGUCAUU
+AAAGCGGGCUAGCCCACCCCAUUGCUUUGGGGGGGUGGGCGAAAAAUAAAAAGGCUGGCC
+UUAGCGCACCCUGUCUUUCGGGAGCGCUAAGGCGAAAAUAAAAAAGAGACUAAGCAUGUA
+GAAACCUUGGCGCUGGGCCCUCCGGACGCGGGUUCGAUUCAAAAAGAGUCGCCCUGGGGG
+GUAACCCCCAGGGGAAAACCCGGCUAAAUCAGGGAAACCCUAACCUGAAAGAAGGCUAGG
+GUAAUCCUGAGGGGUGCCCCGAAACGGGGAACCUGCAGAGACUCUGGCCCCCCUAAAAGG
+GGGGACCAGAUGGGAGGCAAAAUCGUUGAAUAAGUUUUAGAAUGCCUCCCAUAAAACGCC
+GGGCAUCCCGAAAGGGAUGAAGAGAUAGUCCACGCCCCUUGGAAAAUGGGGUAUACGUGU
+CCCGCCACCUCCACCA
+>tmRNA_alpha
+GCCCUUUAAAUUUUAAACAUAUUCUCCUAUAUUAGUAGUGCCGGUUUGCCGGCUAUGGCG
+AUAAACGCCCCGCGUAAUAAACGCAUCGGACCCGGGGGCGGUACCCGGCGCCUCCACCAA
+AAACCUUUCAUUUAUGUGUUUUUUUAUGGGGGCGAAAUAGGAUCGACGAGCGUGUAAAGG
+CGGGGCUUUCGCCCGGUAUGGUGCCACCGUUAUCGGCCCAAAAUUAUAAUUGCAAACGAC
+AACUAUGCUCCGGUUGCUCUUGCUGCGUAAGCAGUUUGAAAAAUUGAAAUUUAAGUCCUA
+AGGGUUAGCACCGUUAGGCGGGGUUCGGGGGCACCUGGCAACAGAAGCCCCCACU
+>tmRNA_beta
+ACACGCAAAUUGACUUGAAGCUGACGGCAACGCGCGUAUAAUCUAGAGCAUGGUUGUAUU
+CCGGCAACCUGGAGGCGUUCUGGACGGGGGUUCGAUUCCCCCCACCUCCACCCAAGGGCA
+UUCCACGGAGAGUGUUUAGAUGGGGGUGUACUGGUUUCGACAGGGCGGGCAAAGGUGAGC
+AGGCAACCCGUCAGGCGACGGACGUUAAUAAUGCAAAUCCAUAAAUGCCAACGAUGAGCA
+UUUCGCAAUGGCCGCCUAAAAACGGCUAGCCGGGGCUGCUGCUGCCUUGUUACCAAAGAG
+CAGCCGGCGGGGGCCUCGGGGCCCCCGCUCA
+>tmRNA_cyano
+CUGUCAGAAUAAAAAUGUCCGGCUUUAGCCGGACUAGGUGACCCACACCACUGUCCCGGA
+CAGCGGUUCGAUUCCGCUCAGCUCCAUUCCUCCUUCUUGGGGCUGCAAUGGUUUCGACGG
+GGCAGAAGGAGGGUGACUGAAGCCUGCUCGGUUAGAGCAAAAACAUAACUGCUAACAACA
+UCGUUAGUUUCUCCCGCCCAGCAGCCCCUGUGGCUGCCUGAGCCUUUAAAGGAGAUGGGG
+CGAGGUCAGCCUUAUCACCCAAAUGACCCAUGGGGCCCGGAAGGGCCC
+>tmRNA_mito
+UAAAUGGACCCAAAGGCAGUAUUUGGUAUUUCCAUAUAAAUUAAAUUAAAAGGGAAUAAU
+AAUAGAAUUGACAUUUA
diff --git a/data/tmrna/cm/all.fa.ndb b/data/tmrna/cm/all.fa.ndb
diff --git a/data/tmrna/cm/all.fa.nhr b/data/tmrna/cm/all.fa.nhr
diff --git a/data/tmrna/cm/all.fa.nin b/data/tmrna/cm/all.fa.nin
diff --git a/data/tmrna/cm/all.fa.njs b/data/tmrna/cm/all.fa.njs
@@ -0,0 +1,22 @@
+{
+  "version": "1.2",
+  "dbname": "all.fa",
+  "dbtype": "Nucleotide",
+  "db-version": 5,
+  "description": "all.fa",
+  "number-of-letters": 2025,
+  "number-of-sequences": 6,
+  "last-updated": "2025-01-21T14:21:00",
+  "number-of-volumes": 1,
+  "bytes-total": 38084,
+  "bytes-to-cache": 675,
+  "files": [
+    "all.fa.ndb",
+    "all.fa.nhr",
+    "all.fa.nin",
+    "all.fa.not",
+    "all.fa.nsq",
+    "all.fa.ntf",
+    "all.fa.nto"
+  ]
+}
diff --git a/data/tmrna/cm/all.fa.not b/data/tmrna/cm/all.fa.not
diff --git a/data/tmrna/cm/all.fa.nsq b/data/tmrna/cm/all.fa.nsq
diff --git a/data/tmrna/cm/all.fa.ntf b/data/tmrna/cm/all.fa.ntf
diff --git a/data/tmrna/cm/all.fa.nto b/data/tmrna/cm/all.fa.nto
diff --git a/data/tmrna/cm/modelinfo.txt b/data/tmrna/cm/modelinfo.txt
@@ -0,0 +1,7 @@
+*all* - - all.cm
+tmRNA tmRNA Bacteria tmRNA.cm
+tmRNA_intron tmRNA Bacteria tmRNA_intron.cm
+tmRNA_alpha tmRNA Alphaproteobacteria tmRNA_alpha.cm
+tmRNA_beta tmRNA Betaproteobacteria tmRNA_beta.cm
+tmRNA_cyano tmRNA Cyanobacteria tmRNA_cyano.cm
+tmRNA_mito tmRNA Eukarya tmRNA_mito.cm
-Original file line number
+Diff line change
@@ Expand Up / @@ -9,4 +9,5 @@ docs/_* @@
     .vscode
     .git
 .4/
+.0/
     .venv/