my last cvs add !

Little convenience script to dump all or nearly ensembl databases by
chromosome, using dump_by_chr.pl.

scripts/dump_all_by_chr.sh

+#!/bin/env bash
+# -*- mode: sh; -*-
+# $Id$
+# Little convenience script to dump all or nearly ensembl databases by
+# chromosome, using dump_by_chr.pl. Current script is meant to be edited,
+# i.e., change to needs.
+#
+
+set -x # be verbose
+
+# . ~/.ensembl-setup # set PERL5LIB etc.; write yourself
+export PERL5LIB
+PERL5LIB=$HOME/head/ensembl/modules:${PERL5LIB:-}
+# only Bio::EnsEMBL::DBLoader; is actually used.
+
+
+chrs="chrY chr19 chr20 chr21 chr22"
+# chrs="chr21"
+user=ensadmin
+pass=ensembl
+host=ensrv3
+# check=
+check="-check" # practically essential when running on new release for first
+
+# 
+litedb=homo_sapiens_lite_120
+core=homo_sapiens_core_120
+fam=homo_sapiens_family_120
+disease=homo_sapiens_disease_120
+maps=homo_sapiens_maps_120
+expression=homo_sapiens_expression_120
+snp=homo_sapiens_snp_120
+embl=homo_sapiens_embl_120
+est=homo_sapiens_est_120
+mouse=homo_sapiens_mouse_120
+
+# alternatively, to do everything in one fell swoop with the -all option
+# (documented in dump_by_chr.pl)
+
+all='homo_sapiens_%s_120'
+
+here=`pwd`
+
+
+timestamp() {
+    echo -n "$1 " "DATE: "; date
+}
+
+# databases=" -dumplite \
+#         -core $core \
+#        -family $fam \
+#        -disease $disease \
+#        -maps $maps \
+#        -expression $expression \
+#        -snp $snp \
+#        -embl $embl \
+#        -est $est \
+#        -mouse $mouse"
+
+databases=" -family $fam \
+       -disease $disease \
+       -maps $maps \
+       -expression $expression \
+       -snp $snp \
+       -embl $embl \
+       -est $est"
+
+timestamp
+for chr in $chrs; do
+    timestamp start
+    cd $here
+    mkdir $chr || true
+    cd $chr
+    touch ../$chr.log # in case it doesn't exist
+
+
+    echo "### starting dump " >> ../$chr.log
+    perl ~/head/ensembl/scripts/dump_by_chr.pl $check \
+        -litedb $litedb \
+        $databases \
+        -u $user -p $pass  -h $host -chr $chr  2>&1 | tee -a ../$chr.log
+
+    timestamp end
+done
+
+
+# ------------------------------------------------------------------------
+# the alternative: 
+# dump_by_chr.pl -litedb homo_sapiens_lite_120 -dumplite  \
+# -all 'homo_sapiens_%s_120' -chr chr22 -h ensrv3 -u ensadmin -p ensembl
+#