# for emacs: -*- mode: sh; -*- # The following are browsers built for BME 230, Spring 2004 class: # Aquifex aeolicus VF5 (bacteria) # Buchnera sp. APS (bacteria) # Methanococcus maripaludis S2 (archaea) # Bordetella bronchiseptica RB50 (bacteria) # Deinococcus radiodurans R1 (bacteria) # Salmonella typhimurium LT2 (bacteria) # Methanopyrus kandleri AV19 (archaea) # Aeropyrum pernix (archaea) # Escherichia coli O157:H7 (bacteria) # Thermoplasma acidophilum (archaea) # Sulfolobus tokodaii (archaea) # Pyrococcus horikoshii (archaea) # Geobacter sulfurreducens PCA (bacteria) # Halobacterium sp. NRC-1 (archaea) # For single chromosome genomes, I just got a script that will set up databases: ssh hgwdev cd ~/kent/src/hg/makeDb/trackDb ~/kent/src/hg/makeDb/bme230.sh aquAeo1 "Aquifex aeolicus VF5" Bacteria ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Aquifex_aeolicus/NC_000918.fna "A. aeolicus VF5" mkdir -p bacteria/aquAeo1 cvs add bacteria bacteria/aquAeo1 ~/kent/src/hg/makeDb/bme230.sh bucBuc1 "Buchnera sp. APS" Bacteria ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Buchnera_sp/NC_002528.fna "B. buchnera APS" mkdir bacteria/bucBuc1 cvs add bacteria/bucBuc1 ~/kent/src/hg/makeDb/bme230.sh metMar1 "Methanococcus maripaludis S2" Archaea ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Methanococcus_maripaludis/NC_005791.fna "M. maripaludis S2" mkdir archae/metMar1 cvs add archae/metMar1 ~/kent/src/hg/makeDb/bme230.sh borBro1 "Bordetella bronchiseptica RB50" Bacteria ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Bordetella_bronchiseptica/NC_002927.fna "B. bronchiseptica RB50" mkdir bacteria/borBro1 cvs add bacteria/borBro1 # some sort of error occurred with this one. i'll try again later. ~/kent/src/hg/makeDb/bme230.sh salTyp1 "Salmonella typhimurium LT2" Bacteria ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Salmonella_typhimurium_LT2/NC_003197.fna "S. typhimurium LT2" mkdir bacteria/salTyp1 cvs add bacteria/salTyp1 ~/kent/src/hg/makeDb/bme230.sh metKan1 "Methanopyrus kandleri AV19" Archaea ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Methanopyrus_kandleri/NC_003551.fna "M. kandleri AV19" mkdir archae/metKan1 cvs add archae/metKan1 ~/kent/src/hg/makeDb/bme230.sh aerPer1 "Aeropyrum pernix" Archaea ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Aeropyrum_pernix/NC_000854.fna "A. pernix" mkdir archae/aerPer1 cvs add archae/aerPer1 ~/kent/src/hg/makeDb/bme230.sh escColH7 "Escherichia coli O157:H7" Bacteria ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_O157H7/NC_002695.fna "E. coli O157:H7" mkdir bacteria/escColH7 cvs add bacteria/escColH7 ~/kent/src/hg/makeDb/bme230.sh theAci1 "Thermoplasma acidophilum" Archaea ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Thermoplasma_acidophilum/NC_002578.fna "T. acidophilum" mkdir archae/theAci1 cvs add archae/theAci1 ~/kent/src/hg/makeDb/bme230.sh sulTok1 "Sulfolobus tokodaii" Archaea ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Sulfolobus_tokodaii/NC_003106.fna "S. tokodaii" mkdir archae/sulTok1 cvs add archae/sulTok1 ~/kent/src/hg/makeDb/bme230.sh pyrHor1 "Pyrococcus horikoshii" Archaea ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Pyrococcus_horikoshii/NC_000961.fna "P. horikoshii" mkdir archae/pyrHor1 cvs add archae/pyrHor1 ~/kent/src/hg/makeDb/bme230.sh geoSul1 "Geobacter sulfurreducens PCA" Bacteria ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Geobacter_sulfurreducens/NC_002939.fna "G. sulfurreducens PCA" mkdir bacteria/geoSul1 cvs add bacteria/geoSul1 ~/kent/src/hg/makeDb/bme230.sh deiRad1 "Deinococcus radiodurans R1" Bacteria ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Deinococcus_radiodurans/NC_001263.fna "D. radiodurans R1" mkdir bacteria/deiRad1 cvs add bacteria/deiRad1 ~/kent/src/hg/makeDb/bme230.sh haloSp1 "Halobacterium sp. NRC-1" Archaea ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Halobacterium_sp/NC_002607.fna "Halobacterium sp. NRC-1" mkdir archae/haloSp1 cvs add archae/haloSp1 # Deal with multi-chrom species: # aquAeo1 extra plasmid ece1 cd /cluster/data/aquAeo1 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Aquifex_aeolicus/NC_001880.fna sed "s/^>.*/>aquAeo1_ece1/" NC_001880.fna > ece1.fa rm NC_001880.fna hgNibSeq aquAeo1 /cluster/data/aquAeo1/nib chr1.fa ece1.fa faSize -detailed ece1.fa >> chrom.sizes mkdir html cd html echo '

About the Aquifex aeolicus VF5 Sequence

chr1 is the main chromosome and corresponds to NC_000918. An extra plasmid is ece1 (NC_001880).

' > description.html ln -s /cluster/data/aquAeo1/html /gbdb/aquAeo1/html echo update dbDb set htmlPath=\"/gbdb/aquAeo1/html/description.html\" where name=\"aquAeo1\" | hgsql -h genome-testdb hgcentraltest # for Buchnera sp. APS... plus i used the wrong scientific name echo update dbDb set organism=\"B. aphidicola str. APS\" where name=\"bucBuc1\" | hgsql -h genome-testdb hgcentraltest cd /cluster/data/bucBuc1 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Buchnera_sp/NC_002252.fna wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Buchnera_sp/NC_002253.fna sed "s/^>.*/>bucBuc1_pTrp/" NC_002252.fna > pTrp.fa sed "s/^>.*/>bucBuc1_pLeu/" NC_002253.fna > pLeu.fa rm NC_002253.fna NC_002252.fna hgNibSeq bucBuc1 /cluster/data/bucBuc1/nib chr1.fa pLeu.fa pTrp.fa faSize -detailed pLeu.fa >> chrom.sizes faSize -detailed pTrp.fa >> chrom.sizes mkdir html cd html echo '

About the Buchnera aphidicola str. APS Sequence

chr1 is the main chromosome and corresponds to NC_002528. Two extra plasmids are pTrp (NC_002252), and pLeu (NC_002253).

' > description.html ln -s /cluster/data/bucBuc1/html /gbdb/bucBuc1/html echo update dbDb set htmlPath=\"/gbdb/bucBuc1/html/description.html\" where name=\"bucBuc1\" | hgsql -h genome-testdb hgcentraltest # Methanococcus maripaludis S2 only has one chrom, but I'll add a description page cd /cluster/data/metMar1/ mkdir html ln -s /cluster/data/metMar1/html /gbdb/metMar1/html cd html echo '

About the Methanococcus maripaludis S2 Sequence

chr1 is the main chromosome and corresponds to NC_005791.

' > description.html echo update dbDb set htmlPath=\"/gbdb/metMar1/html/description.html\" where name=\"metMar1\" | hgsql -h genome-testdb hgcentraltest # Bordetella bronchiseptica RB50 only has one chrom, but I'll add a description page cd /cluster/data/borBro1/ mkdir html ln -s /cluster/data/borBro1/html /gbdb/borBro1/html cd html echo '

About the Bordetella bronchiseptica RB50 Sequence

chr1 is the main chromosome and corresponds to NC_002927.

' > description.html echo update dbDb set htmlPath=\"/gbdb/borBro1/html/description.html\" where name=\"borBro1\" | hgsql -h genome-testdb hgcentraltest # Deinococcus radiodurans R1 has two chroms and two extra plasmids. cd /cluster/data/deiRad1/ wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Deinococcus_radiodurans/NC_001264.fna wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Deinococcus_radiodurans/NC_000958.fna wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Deinococcus_radiodurans/NC_000959.fna sed 's/^>.*/>deiRad1_chr2/' NC_001264.fna > chr2.fa sed 's/^>.*/>deiRad1_MP1/' NC_000958.fna > MP1.fa sed 's/^>.*/>deiRad1_CP1/' NC_000959.fna > CP1.fa rm *.fna hgNibSeq deiRad1 /cluster/data/deiRad1/nib chr1.fa chr2.fa MP1.fa CP1.fa faSize -detailed chr2.fa >> chrom.sizes faSize -detailed MP1.fa >> chrom.sizes faSize -detailed CP1.fa >> chrom.sizes mkdir html ln -s /cluster/data/deiRad1/html /gbdb/deiRad1/html cd html echo '

About the Deinococcus radiodurans R1 Sequence

chr1 and chr2 are the main chromosomes and correspond to NC_001263, and NC_001264 respectively. Two extra plasmids are MP1 (NC_000958) and CP1 (NC_000959).' > description.html echo update dbDb set htmlPath=\"/gbdb/deiRad1/html/description.html\" where name=\"deiRad1\" | hgsql -h genome-testdb hgcentraltest # Salmonella typhimurium LT2 has an extra plasmid cd /cluster/data/salTyp1 wget ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Salmonella_typhimurium_LT2/NC_003277.fna sed 's/^>.*/>salTyp1_pSLT/' NC_003277.fna > pSLT.fa rm NC_003277.fna hgNibSeq salTyp1 /cluster/data/salTyp1/nib chr1.fa pSLT.fa faSize -detailed pSLT.fa >> chrom.sizes mkdir html ln -s /cluster/data/salTyp1/html /gbdb/salTyp1/html cd html echo '

About the Salmonella typhimurium LT2 Sequence

chr1 is the main chromosome (NC_003197) and pSLT is an extra plasmid (NC_003277).' > description.html echo update dbDb set htmlPath=\"/gbdb/salTyp1/html/description.html\" where name=\"salTyp1\" | hgsql -h genome-testdb hgcentraltest # Methanopyrus kandleri AV19 just has one chrom, but I'll add the description: cd /cluster/data/metKan1 mkdir html ln -s /cluster/data/metKan1/html /gbdb/metKan1/html cd html echo '

About the Methanopyrus kandleri AV19 Sequence

chr1 is the main chromosome (NC_003551).' > description.html echo update dbDb set htmlPath=\"/gbdb/metKan1/html/description.html\" where name=\"metKan1\" | hgsql -h genome-testdb hgcentraltest # Aeropyrum pernix just has one chrom, but I'll add the description: cd /cluster/data/aerPer1 mkdir html ln -s /cluster/data/aerPer1/html /gbdb/aerPer1/html cd html echo '

About the Aeropyrum pernix Sequence

chr1 is the main chromosome (NC_000854).' > description.html echo update dbDb set htmlPath=\"/gbdb/aerPer1/html/description.html\" where name=\"aerPer1\" | hgsql -h genome-testdb hgcentraltest # Escherichia coli O157:H7 has one chrom and two plasmids: cd /cluster/data/escColH7 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_O157H7/NC_002128.fna wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_O157H7/NC_002127.fna sed 's/^>.*/>escColH7_pO157/' NC_002128.fna > pO157.fa sed 's/^>.*/>escColH7_pOSAK1/' NC_002127.fna > pOSAK1.fa rm *.fna hgNibSeq escColH7 /cluster/data/escColH7/nib chr1.fa pO157.fa pOSAK1.fa faSize -detailed pO157.fa >> chrom.sizes faSize -detailed pOSAK1.fa >> chrom.sizes mkdir html ln -s /cluster/data/escColH7/html /gbdb/escColH7/html cd html echo '

About the Escherichia coli O157:H7 Sequence

This is the E. coli that makes you sick. chr1 is the main chromosome (NC_002695). In addition there are two plasmids: pOSAK1 (NC_002127) and pO157 (NC_002128).' > description.html echo update dbDb set htmlPath=\"/gbdb/escColH7/html/description.html\" where name=\"escColH7\" | hgsql -h genome-testdb hgcentraltest # Thermoplasma acidophilum has just one chrom: cd /cluster/data/theAci1 mkdir html ln -s /cluster/data/theAci1/html /gbdb/theAci1/html cd html echo '

About the Thermoplasma acidophilum Sequence

chr1 is the main chromosome (NC_002578).' > description.html echo update dbDb set htmlPath=\"/gbdb/theAci1/html/description.html\" where name=\"theAci1\" | hgsql -h genome-testdb hgcentraltest # Sulfolobus tokodaii has just one chrom: cd /cluster/data/sulTok1 mkdir html ln -s /cluster/data/sulTok1/html /gbdb/sulTok1/html cd html echo '

About the Sulfolobus tokodaii Sequence

chr1 is the main chromosome (NC_003106).' > description.html echo update dbDb set htmlPath=\"/gbdb/sulTok1/html/description.html\" where name=\"sulTok1\" | hgsql -h genome-testdb hgcentraltest # Pyrococcus horikoshii has just one chrom cd /cluster/data/pyrHor1 mkdir html ln -s /cluster/data/pyrHor1/html /gbdb/pyrHor1/html cd html echo '

About the Pyrococcus horikoshii Sequence

chr1 is the main chromosome (NC_000961).' > description.html echo update dbDb set htmlPath=\"/gbdb/pyrHor1/html/description.html\" where name=\"pyrHor1\" | hgsql -h genome-testdb hgcentraltest # Geobacter sulfurreducens PCA has just one chrom cd /cluster/data/geoSul1 mkdir html ln -s /cluster/data/geoSul1/html /gbdb/geoSul1/html cd html echo '

About the Geobacter sulfurreducens PCA Sequence

chr1 is the main chromosome (NC_000961).' > description.html echo update dbDb set htmlPath=\"/gbdb/geoSul1/html/description.html\" where name=\"geoSul1\" | hgsql -h genome-testdb hgcentraltest # Halobacterium sp. NRC-1 has 2 extra plasmids cd /cluster/data/haloSp1 wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Halobacterium_sp/NC_001869.fna wget ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Halobacterium_sp/NC_002608.fna sed 's/^>.*/>haloSp1_pNRC100/' NC_001869.fna > pNRC100.fa sed 's/^>.*/>haloSp1_pNRC200/' NC_002608.fna > pNRC200.fa rm *.fna hgNibSeq haloSp1 /cluster/data/haloSp1/nib chr1.fa pNRC100.fa pNRC200.fa faSize -detailed pNRC100.fa >> chrom.sizes faSize -detailed pNRC200.fa >> chrom.sizes mkdir html ln -s /cluster/data/haloSp1/html /gbdb/haloSp1/html cd html echo '

About the Halobacterium sp. NRC-1 Sequence

chr1 is the main chromosome (NC_002607). There are two more plasmids: pNRC100 (NC_001869)and pNRC200 (NC_002608).' > description.html echo update dbDb set htmlPath=\"/gbdb/haloSp1/html/description.html\" where name=\"haloSp1\" | hgsql -h genome-testdb hgcentraltest # so now theres a problem with make alpha. i'm going to make empty trackDb.ra files in # the directories to avoid this. cd ~/kent/src/hg/makeDb/trackDb mkdir bacteria cvs add bacteria for i in aquAeo1 bucBuc1 salTyp1 escColH7 deiRad1 borBro1 geoSul1; do mkdir -p bacteria/$i touch bacteria/$i/trackDb.ra cvs add bacteria/$i cvs add bacteria/$i/trackDb.ra done touch bacteria/trackDb.ra cvs add bacteria/trackDb.ra mkdir archaea cvs add archaea for i in haloSp1 pyrHor1 sulTok1 theAci1 aerPer1 metMar1 metKan1; do mkdir -p archaea/$i touch archaea/$i/trackDb.ra cvs add archaea/$i cvs add archaea/$i/trackDb.ra done touch archaea/trackDb.ra cvs add archaea/trackDb.ra # 04-08-2004: need to add Synecoccus cd ~/kent/src/hg/makeDb/trackDb ~/kent/src/hg/makeDb/bme230.sh synSp1 "Synechococcus sp. WH 8102" Bacteria ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Synechococcus_sp_WH8102/NC_005070.fna "Synechococcus sp. WH 8102" mkdir -p bacteria/synSp1 cvs add bacteria/synSp1 touch bacteria/synSp1/trackDb.ra cd /cluster/data/synSp1 mkdir html ln -s /cluster/data/synSp1/html /gbdb/synSp1/html cd html echo '

About the Synechococcus sp. WH 8102 Sequence

chr1 is the main chromosome (NC_005070).' > description.html echo update dbDb set htmlPath=\"/gbdb/synSp1/html/description.html\" where name=\"synSp1\" | hgsql -h genome-testdb hgcentraltest