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cmdcolincmdcolin
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Lines changed: 91698 additions & 15619 deletions

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‎genark2jbrowse/make.sh‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -199,7 +199,7 @@ if [ "$MODE" = "new" ]; then
199199
process_gff_for_hub() {
200200
local accession="$1"
201201
local input_file
202-
input_file="gff/${accession}_*.gz"
202+
input_file=$(echo gff/"${accession}"_*.gz)
203203
if [ ! -f "$input_file" ]; then
204204
return
205205
fi
@@ -230,7 +230,7 @@ if [ "$MODE" = "new" ]; then
230230
add_track_for_hub() {
231231
local accession="$1"
232232
local gff_file
233-
gff_file="bgz/${accession}_*.gff.gz"
233+
gff_file=$(echo bgz/"${accession}"_*.gff.gz)
234234
if [ ! -f "$gff_file" ]; then
235235
return
236236
fi

‎ucsc2jbrowse/configs/ailMel1.json‎

Lines changed: 189 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1225,6 +1225,195 @@
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"indexType": "CSI"
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}
12271227
}
1228+
},
1229+
{
1230+
"type": "SyntenyTrack",
1231+
"trackId": "ailMel1_to_over.chain.gz_liftOver",
1232+
"name": "ailMel1 to over.chain.gz liftOver",
1233+
"category": ["Pairwise alignments", "liftOver"],
1234+
"assemblyNames": ["ailMel1", "over.chain.gz"],
1235+
"adapter": {
1236+
"type": "PairwiseIndexedPAFAdapter",
1237+
"targetAssembly": "ailMel1",
1238+
"queryAssembly": "over.chain.gz",
1239+
"pifGzLocation": {
1240+
"uri": "liftOver/ailMel1ToCanFam2.over.chain.gz.pif.gz"
1241+
},
1242+
"index": {
1243+
"location": {
1244+
"uri": "liftOver/ailMel1ToCanFam2.over.chain.gz.pif.gz.csi"
1245+
},
1246+
"indexType": "CSI"
1247+
}
1248+
}
1249+
},
1250+
{
1251+
"type": "SyntenyTrack",
1252+
"trackId": "ailMel1_to_over.chain.gz_liftOver",
1253+
"name": "ailMel1 to over.chain.gz liftOver",
1254+
"category": ["Pairwise alignments", "liftOver"],
1255+
"assemblyNames": ["ailMel1", "over.chain.gz"],
1256+
"adapter": {
1257+
"type": "PairwiseIndexedPAFAdapter",
1258+
"targetAssembly": "ailMel1",
1259+
"queryAssembly": "over.chain.gz",
1260+
"pifGzLocation": {
1261+
"uri": "liftOver/ailMel1ToFelCat4.over.chain.gz.pif.gz"
1262+
},
1263+
"index": {
1264+
"location": {
1265+
"uri": "liftOver/ailMel1ToFelCat4.over.chain.gz.pif.gz.csi"
1266+
},
1267+
"indexType": "CSI"
1268+
}
1269+
}
1270+
},
1271+
{
1272+
"type": "SyntenyTrack",
1273+
"trackId": "ailMel1_to_over.chain.gz_liftOver",
1274+
"name": "ailMel1 to over.chain.gz liftOver",
1275+
"category": ["Pairwise alignments", "liftOver"],
1276+
"assemblyNames": ["ailMel1", "over.chain.gz"],
1277+
"adapter": {
1278+
"type": "PairwiseIndexedPAFAdapter",
1279+
"targetAssembly": "ailMel1",
1280+
"queryAssembly": "over.chain.gz",
1281+
"pifGzLocation": {
1282+
"uri": "liftOver/ailMel1ToHg19.over.chain.gz.pif.gz"
1283+
},
1284+
"index": {
1285+
"location": {
1286+
"uri": "liftOver/ailMel1ToHg19.over.chain.gz.pif.gz.csi"
1287+
},
1288+
"indexType": "CSI"
1289+
}
1290+
}
1291+
},
1292+
{
1293+
"type": "SyntenyTrack",
1294+
"trackId": "ailMel1_to_over.chain.gz_liftOver",
1295+
"name": "ailMel1 to over.chain.gz liftOver",
1296+
"category": ["Pairwise alignments", "liftOver"],
1297+
"assemblyNames": ["ailMel1", "over.chain.gz"],
1298+
"adapter": {
1299+
"type": "PairwiseIndexedPAFAdapter",
1300+
"targetAssembly": "ailMel1",
1301+
"queryAssembly": "over.chain.gz",
1302+
"pifGzLocation": {
1303+
"uri": "liftOver/ailMel1ToHg38.over.chain.gz.pif.gz"
1304+
},
1305+
"index": {
1306+
"location": {
1307+
"uri": "liftOver/ailMel1ToHg38.over.chain.gz.pif.gz.csi"
1308+
},
1309+
"indexType": "CSI"
1310+
}
1311+
}
1312+
},
1313+
{
1314+
"type": "SyntenyTrack",
1315+
"trackId": "ailMel1_to_over.chain.gz_liftOver",
1316+
"name": "ailMel1 to over.chain.gz liftOver",
1317+
"category": ["Pairwise alignments", "liftOver"],
1318+
"assemblyNames": ["ailMel1", "over.chain.gz"],
1319+
"adapter": {
1320+
"type": "PairwiseIndexedPAFAdapter",
1321+
"targetAssembly": "ailMel1",
1322+
"queryAssembly": "over.chain.gz",
1323+
"pifGzLocation": {
1324+
"uri": "liftOver/ailMel1ToMm10.over.chain.gz.pif.gz"
1325+
},
1326+
"index": {
1327+
"location": {
1328+
"uri": "liftOver/ailMel1ToMm10.over.chain.gz.pif.gz.csi"
1329+
},
1330+
"indexType": "CSI"
1331+
}
1332+
}
1333+
},
1334+
{
1335+
"type": "SyntenyTrack",
1336+
"trackId": "ailMel1_to_over.chain.gz_liftOver",
1337+
"name": "ailMel1 to over.chain.gz liftOver",
1338+
"category": ["Pairwise alignments", "liftOver"],
1339+
"assemblyNames": ["ailMel1", "over.chain.gz"],
1340+
"adapter": {
1341+
"type": "PairwiseIndexedPAFAdapter",
1342+
"targetAssembly": "ailMel1",
1343+
"queryAssembly": "over.chain.gz",
1344+
"pifGzLocation": {
1345+
"uri": "liftOver/ailMel1ToMm9.over.chain.gz.pif.gz"
1346+
},
1347+
"index": {
1348+
"location": {
1349+
"uri": "liftOver/ailMel1ToMm9.over.chain.gz.pif.gz.csi"
1350+
},
1351+
"indexType": "CSI"
1352+
}
1353+
}
1354+
},
1355+
{
1356+
"type": "SyntenyTrack",
1357+
"trackId": "ailMel1_to_over.chain.gz_liftOver",
1358+
"name": "ailMel1 to over.chain.gz liftOver",
1359+
"category": ["Pairwise alignments", "liftOver"],
1360+
"assemblyNames": ["ailMel1", "over.chain.gz"],
1361+
"adapter": {
1362+
"type": "PairwiseIndexedPAFAdapter",
1363+
"targetAssembly": "ailMel1",
1364+
"queryAssembly": "over.chain.gz",
1365+
"pifGzLocation": {
1366+
"uri": "liftOver/ailMel1ToMonDom5.over.chain.gz.pif.gz"
1367+
},
1368+
"index": {
1369+
"location": {
1370+
"uri": "liftOver/ailMel1ToMonDom5.over.chain.gz.pif.gz.csi"
1371+
},
1372+
"indexType": "CSI"
1373+
}
1374+
}
1375+
},
1376+
{
1377+
"type": "SyntenyTrack",
1378+
"trackId": "ailMel1_to_over.chain.gz_liftOver",
1379+
"name": "ailMel1 to over.chain.gz liftOver",
1380+
"category": ["Pairwise alignments", "liftOver"],
1381+
"assemblyNames": ["ailMel1", "over.chain.gz"],
1382+
"adapter": {
1383+
"type": "PairwiseIndexedPAFAdapter",
1384+
"targetAssembly": "ailMel1",
1385+
"queryAssembly": "over.chain.gz",
1386+
"pifGzLocation": {
1387+
"uri": "liftOver/ailMel1ToRn4.over.chain.gz.pif.gz"
1388+
},
1389+
"index": {
1390+
"location": {
1391+
"uri": "liftOver/ailMel1ToRn4.over.chain.gz.pif.gz.csi"
1392+
},
1393+
"indexType": "CSI"
1394+
}
1395+
}
1396+
},
1397+
{
1398+
"type": "SyntenyTrack",
1399+
"trackId": "ailMel1_to_over.chain.gz_liftOver",
1400+
"name": "ailMel1 to over.chain.gz liftOver",
1401+
"category": ["Pairwise alignments", "liftOver"],
1402+
"assemblyNames": ["ailMel1", "over.chain.gz"],
1403+
"adapter": {
1404+
"type": "PairwiseIndexedPAFAdapter",
1405+
"targetAssembly": "ailMel1",
1406+
"queryAssembly": "over.chain.gz",
1407+
"pifGzLocation": {
1408+
"uri": "liftOver/ailMel1ToRn6.over.chain.gz.pif.gz"
1409+
},
1410+
"index": {
1411+
"location": {
1412+
"uri": "liftOver/ailMel1ToRn6.over.chain.gz.pif.gz.csi"
1413+
},
1414+
"indexType": "CSI"
1415+
}
1416+
}
12281417
}
12291418
],
12301419
"plugins": [

‎ucsc2jbrowse/configs/allMis1.json‎

Lines changed: 42 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1073,6 +1073,48 @@
10731073
"indexType": "CSI"
10741074
}
10751075
}
1076+
},
1077+
{
1078+
"type": "SyntenyTrack",
1079+
"trackId": "allMis1_to_over.chain.gz_liftOver",
1080+
"name": "allMis1 to over.chain.gz liftOver",
1081+
"category": ["Pairwise alignments", "liftOver"],
1082+
"assemblyNames": ["allMis1", "over.chain.gz"],
1083+
"adapter": {
1084+
"type": "PairwiseIndexedPAFAdapter",
1085+
"targetAssembly": "allMis1",
1086+
"queryAssembly": "over.chain.gz",
1087+
"pifGzLocation": {
1088+
"uri": "liftOver/allMis1ToHg19.over.chain.gz.pif.gz"
1089+
},
1090+
"index": {
1091+
"location": {
1092+
"uri": "liftOver/allMis1ToHg19.over.chain.gz.pif.gz.csi"
1093+
},
1094+
"indexType": "CSI"
1095+
}
1096+
}
1097+
},
1098+
{
1099+
"type": "SyntenyTrack",
1100+
"trackId": "allMis1_to_over.chain.gz_liftOver",
1101+
"name": "allMis1 to over.chain.gz liftOver",
1102+
"category": ["Pairwise alignments", "liftOver"],
1103+
"assemblyNames": ["allMis1", "over.chain.gz"],
1104+
"adapter": {
1105+
"type": "PairwiseIndexedPAFAdapter",
1106+
"targetAssembly": "allMis1",
1107+
"queryAssembly": "over.chain.gz",
1108+
"pifGzLocation": {
1109+
"uri": "liftOver/allMis1ToHg38.over.chain.gz.pif.gz"
1110+
},
1111+
"index": {
1112+
"location": {
1113+
"uri": "liftOver/allMis1ToHg38.over.chain.gz.pif.gz.csi"
1114+
},
1115+
"indexType": "CSI"
1116+
}
1117+
}
10761118
}
10771119
],
10781120
"plugins": [

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