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Index of /FortyEight

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File Rev. Age Author Last log entry
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CheckGenome.pm  1.9  19 months  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
ClusterStage.pm  1.3  9 years  mkubal  removed high priority form args
FortyEight.pm  1.4  10 years  paarmann  fixed text
FortyEight.tmpl  1.3  10 years  paarmann  added js for tooltip
GeneralJob.pm  1.1  8 years  olson  New file for general-purpose wokr dir mgmt for jobs.
ImportJob.pm  1.1  9 years  olson  new file
Job48.pm  1.50  4 months  olson  Suppress full name in email if it includes HTML escape
JobError.pm  1.8  4 months  olson  Suppress full name in email if it includes HTML escape
JobStage.pm  1.3  9 years  olson  More stage methods.
JobUpload.pm  1.17  15 months  olson  Revert spurious update from 1.15 to 1.16; add N50 computation.
Makefile  1.39  3 years  olson  Rollup of RASTtk changes.
Mantis.pm  1.5  7 years  olson  Job management fixes.
PipelineUtils.pm  1.3  7 years  olson  more rastq fixes
RawOrganismGenomeBrowser.pm  1.2  10 years  paarmann  *** empty log message ***
SGE.pm  1.3  3 years  olson  Commit latest version of code from production RAST.
SeedExport.pm  1.20  4 months  olson  Truncate long tax entries for EMBL export.
Table.pm  1.6  9 years  parrello  Added TITLE command for Wiki.
TeragridCompute.pm  1.1  9 years  olson  new files
batch_rast.pl  1.13  3 years  olson  Commit latest version of code from production RAST.
boot_rast_servers.pl  1.2  7 years  olson  mods
check_jobs.pl  1.84  14 months  olson  Check for error on old job metadata retrieval during replication setup.
check_jobs_plasmid.pl  1.7  7 years  gdpusch  Fixed call of wrong script instead of `rp_subsystem_coverage_plasmid`
check_jobs_ross.pl  1.1  9 years  overbeek  this is a hacked check_jobs for the ross RAST
check_ncbi.cgi  1.4  10 years  paarmann  *** empty log message ***
check_rast_genome.pl  1.2  9 years  wilke  *** empty log message ***
compute_job_signature.pl  1.5  2 years  olson  Add rasttk workflow to signature.
copy-raw-genome.pl  1.2  10 years  olson  use FIG_Config for jobs direcotry(backend)
crc64.py  1.1  9 years  mkubal  new
create_import_job.pl  1.5  9 years  olson  Rollup of import changes.
dump-rast-data.pl  1.1  6 years  olson  Spreadsheet export, new script for dumping queue data.
find-genomes-not-in-seed.pl  1.3  10 years  olson  move email support to Job48 remove stopligth status make quality_check set up co...
find-orphaned-jobs.pl  1.2  5 years  olson  fixes
get_nmpdr_group.pl  1.1  9 years  olson  Determine NMPDR group name for given genome name.
get_number_of_external_jobs.pl  1.7  8 years  wilke  *** empty log message ***
imp_build_nr.pl  1.3  9 years  olson  Updates to the Teach stuff. Small mod to build_nr to support condtional setting ...
imp_check_tl_sim_status.pl  1.2  9 years  olson  Import changes.
imp_finish_tl_sims.pl  1.6  9 years  olson  lingering fixes for timelogic stuff for the import pipeline.
imp_merge_sims.pl  1.1  9 years  olson  Rollup of RAST->SEED import stuff.
imp_prepare_sims.pl  1.1  9 years  olson  Rollup of RAST->SEED import stuff.
imp_process_sims.pl  1.1  9 years  olson  Rollup of RAST->SEED import stuff.
imp_salvage.pl  1.4  9 years  olson  fix bad salvage bug
imp_sims.pl  1.1  9 years  olson  Rollup of RAST->SEED import stuff.
imp_submit_tl_sims.pl  1.2  9 years  olson  Rollup of import changes.
import_pipeline.pl  1.1  9 years  olson  Rollup of RAST->SEED import stuff.
migrate_job.pl  1.2  10 years  olson  add -new option that assigns a new job number to the migrated job.
pull_sims_from_database.pl  1.2  7 years  olson  support partial sims paths
pull_sims_from_server.pl  1.1  8 years  olson  Add support for pulling sims from sims server and submitting only those that don...
rast-title.xcf  1.1  10 years  paarmann  *** empty log message ***
rast_v1.cgi  1.1  9 years  olson  Add new stuff to mantis support. Rename the v1 rast frontpage to rast_v1.cgi.
rastq.pl  1.5  3 years  olson  Commit latest version of code from production RAST.
replicate_job.pl  1.3  22 months  olson  Don't fail if bbhs missing.
reset-failed-rp.pl  1.8  19 months  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
reset_stage.pl  1.2  7 years  gdpusch  Added code to remove 'CANCEL' file.
rp_CELLO_attribute_generation.pl  1.2  9 years  olson  Don't submit non-TL jobs to the TL queue. Index attributes after new attributes...
rp_CELLO_search.pl  1.3  9 years  mkubal  writes/reads to /rp/genome
rp_HMM_PFAM_search_on_timelogic.pl  1.1  9 years  mkubal  v1
rp_PFAM_attribute_generation.pl  1.2  9 years  olson  Don't submit non-TL jobs to the TL queue. Index attributes after new attributes...
rp_PHOBIUS_attribute_generation.pl  1.2  9 years  olson  Don't submit non-TL jobs to the TL queue. Index attributes after new attributes...
rp_PHOBIUS_search.pl  1.4  9 years  mkubal  new url
rp_PSORT_attribute_generation.pl  1.1  9 years  mkubal  for new RAST genomes
rp_auto_assign.pl  1.17  15 months  olson  Don't do model building until later (export stage)
rp_chunk_sims.pl  1.5  8 years  olson  Add support for pulling sims from sims server and submitting only those that don...
rp_compute_bbhs.pl  1.3  7 years  olson  set metadata in_progress
rp_compute_crc64_for_pegs_in_genome.pl  1.2  9 years  mkubal  for new RAST genomes
rp_compute_pchs.pl  1.5  7 years  olson  set metadata in_progress
rp_compute_peer_sim_pair.pl  1.1  8 years  olson  First working versoin of the peer sims code.
rp_compute_peer_sims.pl  1.2  8 years  olson  First working versoin of the peer sims code.
rp_compute_sims.pl  1.7  5 years  olson  override fixes
rp_correction.pl  1.6  9 years  olson  add -meta=metafile to the invoked processing scripts.
rp_critica.pl  1.4  9 years  olson  set up envirnment for critica perl
rp_gen_teach_sims.pl  1.1  9 years  olson  Updates to the Teach stuff. Small mod to build_nr to support condtional setting ...
rp_genome_phenotype_attribute_generation.pl  1.1  9 years  mkubal  for new RAST genomes
rp_glimmer.pl  1.4  9 years  olson  add the FIG bin and external bin dirs to the path so that run_glimmer2 can find ...
rp_glue_contigs.pl  1.6  18 months  olson  arrange to keep the original annotations written (by rasttk)
rp_index_attributes.pl  1.4  9 years  olson  allow a second argument to be passed & ignored
rp_interpro_computed_attribute_generation.pl  1.1  9 years  mkubal  new
rp_interpro_download_attribute_generation.pl  1.1  9 years  mkubal  new
rp_lustre_finish.pl  1.1  9 years  olson  Support lustre work directory.
rp_make_CELLO_attributes.pl  1.3  9 years  mkubal  writes/reads to /rp/genome
rp_make_PFAM_HMM_derived_attributes.pl  1.4  8 years  olson  use mkdir instead of backticks
rp_make_PHOBIUS_attributes.pl  1.3  9 years  mkubal  writes/reads to /rp/genome
rp_make_PSORT_attributes.pl  1.3  9 years  mkubal  handles possible multilocation pegs
rp_make_genome_phenotype_attributes.pl  1.2  9 years  mkubal  v2
rp_make_interpro_computed_attributes.pl  1.1  9 years  mkubal  new
rp_make_interpro_download_attributes.pl  1.1  9 years  mkubal  new
rp_make_mw_and_pi_attributes.pl  1.5  9 years  mkubal  SeqStat lib fix
rp_make_similar_to_human_attributes.pl  1.2  9 years  mkubal  v2
rp_mw_and_pi_attribute_generation.pl  1.1  9 years  mkubal  new
rp_peer_sim_status.pl  1.2  8 years  olson  First working versoin of the peer sims code.
rp_postproc_sims.pl  1.9  8 years  olson  Add support for pulling sims from sims server and submitting only those that don...
rp_preprocess_sims.pl  1.3  7 years  olson  mods from batch rasting
rp_quality_check.pl  1.13  8 years  olson  commit of random stuff from bob dir
rp_rapid_propagation.pl  1.22  3 years  olson  Rollup of RASTtk changes.
rp_rapid_propagation_classic.pl  1.1  3 years  olson  Add missed files.
rp_rapid_propagation_plasmid.pl  1.1  8 years  arodri7  plasmid rast pipeline first version
rp_rapid_propagation_rasttk.pl  1.6  18 months  olson  Renumber gto file.
rp_request_peer_sims.pl  1.5  13 months  gdpusch  Modified to just warn instead of die if some jobs are not readable.
rp_run_PSORT_on_genome.pl  1.1  9 years  mkubal  for new RAST genomes
rp_run_blast_against_human.pl  1.2  9 years  mkubal  v2
rp_scenarios.pl  1.7  9 years  mkubal  production RAST version
rp_similar_to_human_attribute_generation.pl  1.1  9 years  mkubal  for new RAST genomes
rp_submit_genome_to_iprscan_on_biocluster.pl  1.1  9 years  mkubal  new
rp_submit_sims.pl  1.2  8 years  olson  add hook to set sge priorities based on metadata value. (ported from check_jobs...
rp_subsystem_coverage_plasmid.pl  1.1  8 years  arodri7  added subsystem coverage after auto assign
rp_write_exports.pl  1.14  15 months  olson  Add model reconstruction submission.
rp_write_spreadsheets.pl  1.1  6 years  olson  Spreadsheet export, new script for dumping queue data.
save_job_signature.pl  1.1  7 years  olson  Add job caching support.
send_job_completion_email.pl  1.3  4 months  olson  Don't use HTML fullnames in email.
show_import_list.pl  1.2  7 years  olson  misc updates
shutdown_rast_servers.pl  1.1  7 years  olson  mods from batch rasting
user-upload-report.pl  1.1  4 weeks  olson  User upload file report script.
validate_tl_sims.pl  1.2  9 years  olson  Import changes.

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