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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  23 months  gdpusch  Add test to flip to "metagenome" mode for genomes smaller than 25 kbp, so that P...
ClusterStage.pm  1.3  10 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  9 years  olson  New file for general-purpose wokr dir mgmt for jobs.
ImportJob.pm  1.1  10 years  olson  new file
Job48.pm  1.50  8 months  olson  Suppress full name in email if it includes HTML escape
JobError.pm  1.8  8 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  19 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  8 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  10 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  18 months  olson  Check for error on old job metadata retrieval during replication setup.
check_jobs_plasmid.pl  1.7  8 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  3 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  10 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  6 years  olson  fixes
get_nmpdr_group.pl  1.1  10 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  10 years  olson  Updates to the Teach stuff. Small mod to build_nr to support condtional setting ...
imp_check_tl_sim_status.pl  1.2  10 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  10 years  olson  Rollup of RAST->SEED import stuff.
imp_prepare_sims.pl  1.1  10 years  olson  Rollup of RAST->SEED import stuff.
imp_process_sims.pl  1.1  10 years  olson  Rollup of RAST->SEED import stuff.
imp_salvage.pl  1.4  10 years  olson  fix bad salvage bug
imp_sims.pl  1.1  10 years  olson  Rollup of RAST->SEED import stuff.
imp_submit_tl_sims.pl  1.2  10 years  olson  Rollup of import changes.
import_pipeline.pl  1.1  10 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  2 years  olson  Don't fail if bbhs missing.
reset-failed-rp.pl  1.8  23 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  10 years  olson  Don't submit non-TL jobs to the TL queue. Index attributes after new attributes...
rp_CELLO_search.pl  1.3  10 years  mkubal  writes/reads to /rp/genome
rp_HMM_PFAM_search_on_timelogic.pl  1.1  10 years  mkubal  v1
rp_PFAM_attribute_generation.pl  1.2  10 years  olson  Don't submit non-TL jobs to the TL queue. Index attributes after new attributes...
rp_PHOBIUS_attribute_generation.pl  1.2  10 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  19 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  9 years  olson  First working versoin of the peer sims code.
rp_compute_peer_sims.pl  1.2  9 years  olson  First working versoin of the peer sims code.
rp_compute_sims.pl  1.7  6 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  10 years  olson  set up envirnment for critica perl
rp_gen_teach_sims.pl  1.1  10 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  10 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  22 months  olson  arrange to keep the original annotations written (by rasttk)
rp_index_attributes.pl  1.4  10 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  10 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  10 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  9 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  22 months  olson  Renumber gto file.
rp_request_peer_sims.pl  1.5  16 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  10 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  19 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  8 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 months  olson  User upload file report script.
validate_tl_sims.pl  1.2  10 years  olson  Import changes.

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