NCBI submission: Difference between revisions
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2. buildAssemblyArchive ASSEMBLY.coninfo --prompt --subname umd-20070816-125223 | 2. buildAssemblyArchive ASSEMBLY.coninfo --prompt --subname umd-20070816-125223 | ||
problems: | problems: | ||
conformation: always LINEAR | * submitter_reference="tigr...." : replace tigr with umd | ||
taxid: not recognized | * conformation: always LINEAR : replace LINEAR with CIRCULAR | ||
* taxid: not recognized : replace <taxid>id</taxid> with <organism descriptor="TAXID">id</organism> | |||
3. validate: | 3. validate: | ||
oXygen: software used by NCBI; license required | oXygen: software used by NCBI; license required | ||
xmllint: open source | xmllint: open source | ||
$ xmllint --schema ASSEMBLY.xsd ASSEMBLY.xml > /dev/null | $ xmllint --schema ASSEMBLY.xsd ASSEMBLY.xml > /dev/null | ||
Revision as of 18:24, 17 August 2007
NCBI
seqin: standalone application
Compressed archive containing 2 files: ASSEMBLY.xml , MD5 Accepted only by uploading to NCBI FTP server. server: ftp-private.ncbi.nlm.nih.gov login: umd_trc passwd: center: UMD description: University of Maryland ASSEMBLY XML Schema png ASSEMBLY XML Schema xsd
Procedure
Files:
.contig, .seq, .qual, .seq_name2ti
Steps:
1. makeConinfo ASSEMBLY.coninfo
2. buildAssemblyArchive ASSEMBLY.coninfo --prompt --subname umd-20070816-125223
problems:
* submitter_reference="tigr...." : replace tigr with umd
* conformation: always LINEAR : replace LINEAR with CIRCULAR
* taxid: not recognized : replace <taxid>id</taxid> with <organism descriptor="TAXID">id</organism>
3. validate: oXygen: software used by NCBI; license required xmllint: open source $ xmllint --schema ASSEMBLY.xsd ASSEMBLY.xml > /dev/null