# ##################################################
# A. General pipeline for updating the Atlas #
# ##################################################
# 2017-07-29 Dessen Philippe (
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)
#
# all scripts are running in $CYT_DIR/Scripts directory
#
#!/usr/bin/bash
# ===============================================================
# AUTHOR : P. DESSEN
# DATE : Mon Aug 2 18:27:27 MET DST 1999
# FILE : maj_full.sh
# GOAL : Automatic updating of html files from txt files
# RUN : ./maj_full.sh 2>/dev/null > indexation.log &
# ===============================================================
cd $CYT_DIR/Scripts
date1=`date`
echo "start " $date1
# I. Generation of Genes links from Anomalies, Tumors, Kprones
# =============================================================
# Identification of all links (CC: TXT: ID: > in all txt files
./ident_hyper.pl
# Generation of several files
# hyper_Genes0.txt
# hyper_Anomalies.txt
# hyper_Tumors.txt
# hyper_Kprones.txt
# followed by concatenation in ./Scripts/Data/hyper_All.txt
# creation of Data if does exist
./otheranom_gene2.pl
# otheranom_gene2.pl in Scripts
# creation of an html bloc in Genes html_files
# with relation with Anomalies files
# Generation of id.html files in the directory
# ../Genes/AnomLinks/1.html
# 2 distinct extracts
# 1. genes associated with a FUSION_GENE in Anom files
# 2. genes associated with Anom in hyperlinks <CC: TXT: ID:>
# use the file ./Data/hyper_All.txt
# and the file ./genes_gc.txt (indexation of filename with NAME)
./othertumor_gene2.pl
# othertumor_gene.pl dans Scripts
# creation of an html bloc in Genes html_files
# with relation with Tumors files
# Generation of id.html files in the directory
# ../Genes/TumorsLinks/1.html
# 2 distinct extracts
# 1. genes associated with FUSION_GENE in the Tumors files
# 2. genes associated with Tumors in hyperlinks <CC: TXT: ID:>
./otherkprone_gene2.pl
# otherkprone_gene2.pl in Scripts
# creation of an html bloc in Genes html_files
# Generation of id.html files in the directory
# ../Genes/KpronesLinks/10001.html
# 2 distinct extractions
# 1. genes associated with SYMBOL dans les fiches Kprones
# 2. genes associated with Kprones in hyperlinks <CC: TXT: ID:>
./othergene_anom.pl
# othergene_anom.pl id_chrom_clin in Scripts
# creation of a html bloc html for Anomalies
# in the directory
# ../Anomalies/GeneLinks/1001.html
./othertransloc_anom.pl
# othertransloc_anom.pl in Scripts
# creation of a transloc html bloc for Anomalies
# Validation in first the creation of the fil
# ./Data/hyper_translocAll.txt
# with the script extract_transloc_name.pl
#
# Generation of links files of transloc files with Anomalies
# File created by extract_transloc_name.pl from
# ./Data/hyper_translocAll.txt
./othergene_tumor.pl
# othergene_tumor.pl dans Scripts
# uses the file ./Data/hyper_All.txt
# creation of an html bloc for Tumors in
# ../Tumors/GeneLinks/5001.html
# Generation of links of Genes files with Tumors
# File created by extract_gene_name.pl from
# ./Data/hyper_All.txt
#
require "./miscfct.pl"; # fonctions diverses
require "gereDbid.pl"; # -- pour l'id des genes
./cytatlas
$ ls -ld */*Links
drwxrwxr-x+ 1 phd None 0 1 juil. 09:28 Anomalies/GeneLinks
drwxrwxr-x+ 1 phd None 0 1 juil. 09:24 Genes/AnomLinks
drwxrwxr-x+ 1 phd None 0 1 juil. 09:27 Genes/KproneLinks
drwxrwxr-x+ 1 phd None 0 1 juil. 09:27 Genes/TumorLinks
drwxrwxr-x+ 1 phd None 0 1 juil. 09:28 Tumors/GeneLinks
#
# II. Generation of Genes txt and html files
# ==========================================
rm ../Genes/GC_*.txt
rm -f ../../chromcancer/Genes/GC_*.html
# for the 2 sets of non annotated genes
./gen_genes_gn.sh
./gen_genes_gc.sh
# for the set of experted genes (Genes0)
./gen_gene2.sh
# creation of links from GC_annot_genes to AtlasFilename
# This permits to address url either bt AtlasFilename or by
# symolic url "GC_<symbol>.html"
./gen_genes_link.sh
#
# III. indexation
# ===============
./indexation.sh
#
# IV. Generation of all html files
# ================================
# preliminary
# generation of preliminary files LK_xxx.html , TU_xxx.html ..
# for forsale files
./maj_prelim.sh
#
# generation of html cards files
./gen_anom.sh
./gen_kprone.sh
./gen_tumor.sh
./gen_report.sh
./gen_educ.sh
./gen_deep.sh
#./gen_study.sh
# chromosome pages indexation
./index_bychrom3.pl
# reindexation (second round : not mandatory ?)
./indexation.sh
# regeneration of html cards (after reindexation)
./gen_gene2.sh
./gen_anom.sh
./gen_kprone.sh
./gen_tumor.sh
./gen.educ.sh
./gen_deep.sh
./gen_report.sh
# Management of images
cp_anom_img.sh
cp_deep_img.sh
cp_educ_img.sh
cp_genes_img.sh
cp_kpr_img.sh
cp_report_img.sh
cp_tum_img.sh
date2=`date`
echo "end " $date2
echo "maj_full.sh " $date1 $date2
echo "==================================="
#
mail -s "Atlas_IGR__maj_full "
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< nohup.out
mail -s "Atlas_IGR__maj_full "
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< indexation.log
# ##################################
# B. Indexation procedure #
# ##################################
# Use indexation.sh after any modifications on cards to maintain
# updated indexes and links
# indexation.sh
#!/bin/bash
# ==============================================================
# AUTHOR : P.DESSEN
# DATE : 11.12.99
# FILE :./indexation.sh
# GOAL : automatic generation of indexes and catalogs
# ex: ./indexation.sh 2 >/dev/null > indexation_20160306.log &
# to be run in $CYT_DIR/Scripts
# ==============================================================
# ------------------------------------------------
# ATLAS environnement variables
# ------------------------------------------------
# CYT_DIR needs to be defined (in $HOME/cytatlas.sh)
# CYT_DIR='..'
source $HOME/cytatlas.sh
GENE_DIR=$CYT_DIR/Genes
ANOM_DIR=$CYT_DIR/Anomalies
TUMOR_DIR=$CYT_DIR/Tumors
KPRON_DIR=$CYT_DIR/Kprones
REPORT_DIR=$CYT_DIR/Reports
STUDY_DIR=$CYT_DIR/StudyGroup
DEEP_DIR=$CYT_DIR/Deep
EDUC_DIR=$CYT_DIR/Educ
WGENE_DIR=$CYTW_DIR/Genes
WANOM_DIR=$CYTW_DIR/Anomalies
WTUMOR_DIR=$CYTW_DIR/Tumors
WKPRON_DIR=$CYTW_DIR/Kprones
WREPORT_DIR=$CYTW_DIR/Reports
WDEEP_DIR=$CYTW_DIR/Deep
WEDUC_DIR=$CYTW_DIR/Educ
WCOLLAB_DIR=$CYTW_DIR/Collab
SCRIPT_DIR=$CYT_DIR/Scripts
export GENE_DIR ANOM_DIR TUMOR_DIR KPRON_DIR SCRIPT_DIR
export REPORT_DIR STUDY_DIR DEEP_DIR EDUC_DIR
export WGENE_DIR WANOM_DIR WTUMOR_DIR WKPRON_DIR
export WREPORT_DIR WDEEP_DIR WEDUC_DIR WCOLLAB_DIR
# ----------------------------------------------
echo "--------------------------------------------------------"
echo " Atlas indexation
echo "`date`
echo "--------------------------------------------------------"
DATEIN=`date`
# pretraitment
# Regeneration of GC.txt files_
echo "Generation of GC_xxx.txt files "
echo "the genes_gc.txt and genes_gn.txt files need to be updated\n"
perl $CYT_DIR/Scripts/gener_gc.pl genes_gc.txt 2>/dev/null
perl $CYT_DIR/Scripts/gener_gc.pl genes_gn.txt 2>/dev/null
ls -l genes_gc.txt
ls -l genes_gn.txt
# ----------------------------------------------------------
# Build of the database of all objects of Atlas
# ObjDB.txt contains the list
# ----------------------------------------------------------
echo "Build of the database ObjDB.txt"
echo "`date`";
perl $CYT_DIR/Scripts/x_id.pl # build if ObjDB.txt
ls -l ObjDB.txt
# ----------------------------------------------------------
# Build of the Genes : file ObjDB0.txt
perl $CYT_DIR/Scripts/majgene.pl 2>/dev/null #
ls -l ObjDB0.txt
# ----------------------------------------------------------
# catalog maintains several features of each card
echo "Creation of a catalog"
perl $CYT_DIR/Scripts/catalog.pl 2>/dev/null #
ls -l catalog
# ----------------------------------------------------------
# reconstruction des index divers
echo "Build of ObjDB1.txt and ObjDB2.txt"
perl $CYT_DIR/Scripts/majfich.pl 2>/dev/null #
ls -l ObjDB1.txt
ls -l ObjDB2.txt
echo "Build of ObjDB1.html"
perl $CYT_DIR/Scripts/majfich2.pl 2>/dev/null #
echo "Build of ObjDB3.txt and ObjDB4.txt"
perl $CYT_DIR/Scripts/majfich3.pl 2>/dev/null #
ls -l ObjDB3.txt
ls -l ObjDB4.txt
echo "Build of ObjDB5.txt (correlation anom tumor genes) and ObjDB7.txt"
perl $CYT_DIR/Scripts/majfich5.pl 2>/dev/null
ls -l ObjDB5.txt
# ----------------------------------------------------------
# Generation of tabulated files for catalog and forsale
# catalog_out.txt and forsale_out.txt
perl $CYT_DIR/Scripts/forsale_out.pl forsale 2>/dev/null # perl $CYT_DIR/Scripts/forsale_out.pl catalog 2>/dev/null #
ls -l forsale_out.txt
ls -l catalog_out.txt
# ----------------------------------------------------------
# modification of catalog_out.txt depending of the reserved file
perl $CYT_DIR/Scripts/reserved.pl
# ----------------------------------------------------------
# concatenation of catalogs (catalog + forsale)
cat $CYT_DIR/Scripts/catalog_out.txt > catalog_full.txt
cat $CYT_DIR/Scripts/forsale_out.txt >> catalog_full.txt
ls -l catalog_full.txt
# Generation of a expertized Gene file
grep GENE ../../chromcancer/Collab/catalog_out.txt | awk -F\t '{print $3,"\t",$5} ' |grep -v GC_ > gce.txt
# ----------------------------------------------------------
#
echo "============= End of rebuild ================"
# ----------------------------------------------------------
# --- Indexations -----
# creation of several indexes for Genes
# index of genes by symbol
# index of objects by chromosome.
# ----------------------------------------------------------
echo " "
echo " --- Indexation des genes ---"
cd $GENE_DIR
$CYT_DIR/Scripts/index_gene2.pl 2>/dev/null > $WGENE_DIR/Geneliste.html
ls -l $WGENE_DIR/Geneliste.html
cd $CYT_DIR/Scripts
$CYT_DIR/Scripts/index_genes_red.pl
echo " "
echo " --- Indexation of Anomalies ---"
$CYT_DIR/Scripts/index_anom2.pl 2>/dev/null > $WANOM_DIR/Anomliste.html
$CYT_DIR/Scripts/index_lymphoma.pl 2>/dev/null > $WANOM_DIR/Lymphomaliste.html
$CYT_DIR/Scripts/index_myeloid.pl 2>/dev/null > $WANOM_DIR/Myeloidliste.html
ls -l $WANOM_DIR/Anomliste.html
ls -l $WANOM_DIR/Lymphomaliste.html
ls -l $WANOM_DIR/Myeloidliste.html
echo " "
echo " --- Indexation of Tumors ---"
cd $TUMOR_DIR
$CYT_DIR/Scripts/index_tumor2.pl 2>/dev/null > $WTUMOR_DIR/Tumorliste.html
ls -l $WTUMOR_DIR/Tumorliste.html
cd $CYT_DIR/Scripts
$CYT_DIR/Scripts/solid_section.pl 2>/dev/null
echo " "
echo " --- Indexation of Kprones ---"
cd $KPRON_DIR
$CYT_DIR/Scripts/index_kprone.pl 2>/dev/null > $WKPRON_DIR/Kproneliste.html
ls -l $WKPRON_DIR/Kproneliste.html
echo " "
echo " --- Indexation of Reports ---"
cd $REPORT_DIR
$CYT_DIR/Scripts/index_report.pl 2>/dev/null > $WREPORT_DIR/Reportliste.html
ls -l $WREPORT_DIR/Reportliste.html
echo " --- Indexation of Deep ---"
cd $DEEP_DIR
$CYT_DIR/Scripts/index_deep.pl 2>/dev/null > $WDEEP_DIR/deeplist.html
ls -l $WDEEP_DIR/deeplist.html
cd $CYT_DIR/Scripts
chmod a+r $CYTW_DIR/Genes/Geneliste.html
chmod a+r $CYTW_DIR/Anomalies/Anomliste.html
chmod a+r $CYTW_DIR/Tumors/Tumorliste.html
chmod a+r $CYTW_DIR/Kprones/Kproneliste.html
chmod a+r $CYTW_DIR/Reports/Reportliste.html
chmod a+r $CYTW_DIR/Deep/deeplist.html
# ----------------------------------------------------------
#
## echo " "
## echo "--- Indexation of GeneLink ---"
#### Normally done in maj_full.sh #####
#### $CYT_DIR/Scripts/ident_hyper.pl
#### $CYT_DIR/Scripts/othergene_anom.pl
#### $CYT_DIR/Scripts/othergene_tumor.pl
#### $CYT_DIR/Scripts/othergene_kprone.pl
#### $CYT_DIR/Scripts/otheranom_gene2.pl
#### $CYT_DIR/Scripts/othertransloc_anom.pl
#### $CYT_DIR/Scripts/othertumor_gene2.pl
#### $CYT_DIR/Scripts/otherkprone_gene2.pl
# ----------------------------------------------------------
#
echo " "
echo " --- Mitelman Files ---"
cd $CYT_DIR/Scripts
$CYT_DIR/Scripts/report2mitelman.pl 2> /dev/null
$CYT_DIR/Scripts/report2mitelman2.pl2> /dev/null
$CYT_DIR/Scripts/a0_mitel2jlh.pl > ../../chromcancer/Collab/mitelman_anom.txt
echo ""
# ----------------------------------------------------------
#
#echo " ----- Indexation of Genes GC --- "
#cd $CYT_DIR/Scripts
#perl $CYT_DIR/Scripts/index_genes_gc.sh
# ----------------------------------------------------------
#
echo " "
echo " --- Indexation by chrom ---"
cd $CYT_DIR/Scripts
perl $CYT_DIR/Scripts/index_bychrom3.pl 2> /dev/null
perl $CYT_DIR/Scripts/index_genes_chromg.pl 2>/dev/null
echo " "
echo " --- Creation of th file cytoentities.html ---"
perl $CYT_DIR/Scripts/cytoentities.pl 2> /dev/null
perl $CYT_DIR/Scripts/cytoentities2.pl 2> /dev/null
# ----------------------------------------------------------
### echo " --- Indexation of the file hugo2url.dat ---"
### perl $CYT_DIR/Scripts/hugo2url.pl
# ----------------------------------------------------------
echo " "
echo " --- Creation of file GeneExtlnk.txt ---"
perl $CYT_DIR/Scripts/extlnk2.pl Genes 2>/dev/null
echo " "
echo " --- Creation of file GeneExtlnk.html ---"
perl $CYT_DIR/Scripts/extlnk3.pl Genes 2>/dev/null
echo " "
echo " --- Creation of file GeneLink.txt ---"
perl $CYT_DIR/Scripts/extlnk4.pl Genes
# ----------------------------------------------------------
## indexation des authors
cd $CYT_DIR/Scripts
perl indxauth.pl 2>/dev/null
ls -l IndxAuth.txt
perl indxauth2.pl 2>/dev/null
ls -l indxauth2.pl
ls -l IndxAuth.html
ls -l IndxAuth2.txt
echo "Be careful : the key_date_pays.txt file may be updated...."
ls -l key_date_pays.txt
echo "Indexation IndxAuth3.txt "
perl indxauth3.pl 2>/dev/null
ls -l IndxAuth3.txt
echo "Indexation IndxAuth4.txt "
perl traitauth.pl 2>/dev/null > ./IndxAuth4.txt
ls -l IndxAuth4.txt
echo "Indexation IndxAuth5.txt "
perl indxauth5.pl 2>/dev/null
ls -l IndxAuth5.txt
echo "Indexation IndxAuth6.txt "
perl indxauth6.pl 2>/dev/null
ls -l IndxAuth6.txt
echo "Indexation IndxAuth1.txt "
perl indxauth1.pl 2>/dev/null
ls -l IndxAuth1.txt
## copies of authors indexes in Collab (Archive)
echo "mv to ../../chromcancer/Collab "
mv IndxAuth.txt $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth.txt
mv IndxAuth.html $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth.html
mv IndxAuth2.txt $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth2.txt
mv IndxAuth2.html $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth.html
mv IndxAuth3.txt $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth3.txt
mv IndxAuth4.txt $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth4.txt
mv IndxAuth5.txt $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth5.txt
mv IndxAuth6.txt $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth6.txt
mv IndxAuth1.txt $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth1.txt
mv IndxAuth1.html $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxAuth1.html
cp -p key_date_pays.txt $CYTW_DIR/Collab
# ----------------------------------------------------------
# Generation of Nosology
echo "Reconsruction des Nosology"
perl $CYT_DIR/Scripts/solid_nosology2.pl 2>/dev/null
ls -l $CYTW_DIR/Tumors/Solid_Nosol*.html
# ----------------------------------------------------------
## indexation des images
echo "Indexation of images"
perl $CYT_DIR/Scripts/indximg.pl 2>/dev/null
cp -p $CYT_DIR/Scripts/IndxImg.txt $CYTW_DIR/Collab
ls -l $CYTW_DIR/Collab/IndxImg.txt
# ----------------------------------------------------------
### indexation of PMID
echo "Indexation of PMID"
perl $CYT_DIR/Scripts/parsing_med.pl 2>/dev/null
## indexation of bibliographic references
echo "indexation of bibliographic references"
perl $CYT_DIR/Scripts/parsing_ref.pl 2/dev/null > ../../chromcancer/Collab/url_ref.txt
ls -l ../../chromcancer/Collab/url_ref.txt
## indexation of bibliographic references
echo "indexation of bibliographic references"
perl $CYT_DIR/Scripts/parsing_biblio.pl 2>/dev/null > ../../chromcancer/Collab/parsing_biblio.txt
ls -l ../../chromcancer/Collab/parsing_biblio.txt
# ----------------------------------------------------------
cd $CYT_DIR/Scripts
echo "copies dans ../../chromcancer/Collab"
# copies in ../../chromcancer/Collab
## copy des ObjDB.txt dans $CYTW_DIR/Collab/
cp -p ObjDB*.txt $CYTW_DIR/Collab
## copy of ObjDB1.html in $CYTW_DIR/Collab/
mv ObjDB*.html $CYTW_DIR/Collab
## copy of GeneExtlnk.txt in $CYTW_DIR/Collab/
mv GeneExtlnk.txt $CYTW_DIR/Collab
mv GeneExtlnk.html $CYTW_DIR/Collab
##mv $CYT_DIR/Scripts/GeneLink.txt $CYTW_DIR/Collab
## copy of cytoentities.html
## copie of tabulated files : forsale et catalog
cp forsale_out.txt $CYTW_DIR/Collab
cp catalog_out.txt $CYTW_DIR/Collab
cp forsale $CYTW_DIR/Collab
cp catalog $CYTW_DIR/Collab
cp catalog_full.txt $CYTW_DIR/Collab
## copie du fichier genes_cancer.txt
cp -p genes_gc.txt $CYTW_DIR/Collab
cp -p genes_gn.txt $CYTW_DIR/Collab
cp -p genes_gcr.txt $CYTW_DIR/Collab
## copy of genes non_cancer
cp -p genes_gn.txt $CYTW_DIR/Collab
# copy of parsing_med
cp -p list_refmedline.txt $CYTW_DIR/Collab
#
chmod 664 $CYTW_DIR/Collab/*.txt
chmod 664 $CYTW_DIR/Collab/*.html
# ----------------------------------------------------------
# generation of the genes atlas file
echo "Generation du fichier gene_atlas.txt "
filtcol genes_gc.txt 45 "<>" "-" > $CYTW_DIR/Collab/genes_atlas.txt
ls -l $CYTW_DIR/Collab/genes_atlas.txt
# ----------------------------------------------------------
# generation of the humprot_atlas.txt file
prtab $CYTW_DIR/Collab/genes_atlas.txt 1 2 10-12 22-23 46 > $CYTW_DIR/Collab/humprot_atlas.txt
echo "generation of the humprot_atlas.txt file"
ls -l $CYTW_DIR/Collab/humprot_atlas.txt
# ----------------------------------------------------------
## copy of Amplicons
echo "copy of amplicons"
cp -p $CYT_DIR/Ampl/*.html $CYTW_DIR/Ampl
cp -p $CYT_DIR/Ampl/Images/*.jpg $CYTW_DIR/Ampl/Images
# ----------------------------------------------------------
# Categories
# indexation of images
cd $CYT_DIR/Scripts
echo "indexation of categories "
cd $CYT_DIR/Scripts/Data/Category_editor
./prepcat2.sh
cd $CYT_DIR/Scripts
$CYT_DIR/Scripts/indximgcategory.pl 2>/dev/null
$CYT_DIR/Scripts/index_category2.pl 2>/dev/null
ls -l Categories_img.txt
ls -l category_img.txt
ls -l category_lst.txt
cp -p catdeepgene.txt $CYTW_DIR/Collab/catdeepgene.txt
cp -p Categories_img.txt $CYTW_DIR/Collab/Categories_img.txt
cp -p category_img.txt $CYTW_DIR/Collab/
cp -p category_lst.txt $CYTW_DIR/Collab/
# ----------------------------------------------------------
# generation of atlas_statuts
perl $CYT_DIR/Scripts/atlas_status.pl 2> /dev/null
echo "rebuild of Status directories"
ls -l $CYTW_DIR/Status/Status_*html
# ----------------------------------------------------------
# Indexation of ICD
perl $CYT_DIR/Scripts/index_icd_topo.pl 2> /dev/null
perl $CYT_DIR/Scripts/index_icd_morph.pl 2> /dev/null
# ----------------------------------------------------------
# Update of recents files (2 years)
echo "Update of recents files (2 years) "
# lastfiles : Report.html
$CYT_DIR/Scripts/lastfile.pl 2>/dev/null
ls -l $CYTW_DIR/Recent.html
# ----------------------------------------------------------
# Statfiches
echo "statfiches "
$CYT_DIR/Scripts/statfiches.pl 2>/dev/null
ls -l $CYTW_DIR/Collab/StatFiches.html
# ----------------------------------------------------------
# Update of Backpage
# modifBackpage creates a Backpage2.html file
# the addlist file contains new authors
#$CYT_DIR/Scripts/modifBackpage addlist
#cp $CYTW_DIR/BackpageAbout.html $CYTW_DIR/BackpageAbout0.html #mv $CYTW_DIR/BackpageAbout2.html $CYTW_DIR/BackpageAbout.html
cp $CYT_DIR/Scripts/listeAuthBPage.txt $CYTW_DIR/Collab/
# ----------------------------------------------------------
# creation of a synthesis file JLH ObjDB6.txt
echo "creation of ObjDB6.txt "
majfich4.pl 2>/dev/null
ls -l $CYTW_DIR/Collab/ObjDB6.txt
# ----------------------------------------------------------
# List of regular updates (depending of releases)
# creation of chromcancer/cosmic_study.html
# read of ../Standards/COSMIC/cosmic_study.txt
./cosmic2html.pl
#
# ICGC : list of projects
# creation of ../../chromcancer/icgc_projects.html
# Lecture de ../TCGA_ICGC/ICGC/cgc_projects.txt
./icgc2html.pl
#
# copies of the Band files
cp $CYT_DIR/Scripts/tmp_allgenes.txt $CYTW_DIR/Collab
cp $CYT_DIR/Scripts/tmp_allanom.txt $CYTW_DIR/Collab
cp $CYT_DIR/Scripts/anom_bandall.txt $CYTW_DIR/Collab
cp $CYT_DIR/Scripts/gene_bandall.txt $CYTW_DIR/Collab
# list of files on archive ( Collab )
echo "list of files on archive $CYTW/Collab "
ls -lt $CYTW_DIR/Collab
# Update of the data on index.html
# Sun Aug 12 12:09:46 MEST 2007
# Sat Nov 21 10:28:10 MET 2009
# Thu Jul 9 15:36:42 MEST 2015
DATEOUT=`date`
# to be adapted to time/date format (depending of UNIX)
perl -pi.bak -ne 's@\S+ \S+ \d+ \d+:\d+:\d+ MEST 20\d\d@$DATEOUT@' $CYTW_DIR/index.html
rm $CYTW_DIR/index.html.bak
echo "start of indexation $DATEIN"
echo "end of indexation $DATEOUT"
# ----------------------------------------------------------
# statistics
$CYT_DIR/Scripts/stat_atlas.pl > $CYTW_DIR/stat_atlas.html
#
echo "Do not forgot to update the key_date_pays.txt file"
ls -l key_date_pays.txt
# Update of the MySQL indexation (only on INIST)
# ----------------------------------------------------------
############################################################