Docs: Database and Guix

2 files changed, 351 insertions, 0 deletions

diff --git a/doc/GUIX-archive.org b/doc/GUIX-archive.org
new file mode 100644
index 00000000..67ab5cd0
--- /dev/null
+++ b/doc/GUIX-archive.org
@@ -0,0 +1,106 @@
+* Binary deployment
+
+Note binary deployment is not working pending a few improvements
+to GNU Guix. See source deployment instead.
+
+** Install Guix using a tar ball
+
+GN can be deployed either as a binary tarball or as a GNU Guix
+package. First install GNU Guix following the instructions of the
+[[https://www.gnu.org/software/guix/manual/html_node/Binary-Installation.html#Binary-Installation][binary installation]] using a tar ball from [[https://www.gnu.org/software/guix/download/][here]].
+
+With guix-daemon running you should be able to install the hello
+package:
+
+: guix package -i hello
+
+** Fix locale
+
+You may want to 
+
+#+begin_src sh   :lang bash
+export GUIX_LOCPATH=$HOME/.guix-profile/lib/locale
+export LC_ALL=en_US.utf8
+#+end_src sh   :lang bash
+
+** Authorize our archives
+
+Next add our archive key to guix (as root):
+
+#+begin_src scheme
+echo "(public-key   
+ (ecc 
+  (curve Ed25519)
+  (q #E9A95686D8437186302E07C7AB9BF3913F435026C2D389AF27D9C66FD6EBB649#)
+  )
+ )
+"|guix archive --authorize
+#+end_src scheme
+
+if you have trouble finding a suitable guix try
+
+: ls /gnu/store/*guix-*/bin/guix
+
+and you should be able to use this directly, e.g.
+
+: alias guix=/gnu/store/632msbms2yaldfnlrb5lbnlnmn9yjisw-guix-0.9.0/bin/guix
+: guix --version
+
+** Download and install the GN2 archive
+
+Find the archive on 
+
+  http://files.genenetwork.org/software/
+
+download and install with
+
+#+begin_src bash
+guix archive --import < genenetwork2-data-hash.nar
+#+end_src bash
+
+and you should see a list of packages installing, e.g.
+
+#+begin_src bash
+importing path `/gnu/store/l1zs2drn3zdzl5ysjcmhibcpa35p9zfc-python2-mysqlclient-1.3.7'
+importing path `/gnu/store/n7kfg4knibvblggy8ci2liscl7vz5wkg-python2-parallel-1.6.4'
+importing path `/gnu/store/qvv16qwlq59gp5d07lwbf5n8ndsi3il3-python2-sqlalchemy-1.0.11'
+importing path `/gnu/store/qw872mbmr9ir0a9drv9xw9pvjk05ywwy-python2-xlsxwriter-0.8.4'
+importing path `/gnu/store/wc112m1xfy3p08v14bdzay2ki2rirdsm-pylmm-gn2-1.0-3c6d1cac8'
+importing path `/gnu/store/zfkcy17c2ks3cd9ks14irdabqvmlfpyn-python2-flask-sqlalchemy-2.1'
+importing path `/gnu/store/cgcjdiz1qylbc372gc3nda3372ihkpqb-genenetwork2-2.0-a8fcff4'
+(etc.)
+#+end_src bash
+
+The following packages need to be added and the R path set
+
+: export R_LIBS_SITE="/home/wrk/.guix-profile/site-library/"
+: guix package -i /gnu/store/w0dqg9dshq53j8xhcnqgvnvms2s6y5k5-r-wgcna-1.49-425bc170cc0873ddbd414675ac40f6d4d724c7cb
+: guix package -i /gnu/store/k60bdlm0v7xic88j2z5c1jb1jvc371mn-r-qtl-1.38-4
+
+You can add the last one to your profile
+
+: guix package -i /gnu/store/cgcjdiz1qylbc372gc3nda3372ihkpqb-genenetwork2-2.0-a8fcff
+: export PATH=~/.guix-profile/bin:$PATH
+: genenetwork2
+
+ or run it directly with
+
+: /gnu/store/cgcjdiz1qylbc372gc3nda3372ihkpqb-genenetwork2-2.0-a8fcff/bin/genenetwork2
+
+
+
+** Other
+
+Update guix with a 'guix pull' and make guix visible in the path.
+More information exists also in my [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org][guix-notes]].
+
+With guix running you should be able to install python, for example.
+
+: guix package -i python2
+
+This will make python appear in $HOME/.guix-profile/bin/python. Suggested
+environment settings can be seen with
+
+: guix package --search-paths
+
+
diff --git a/doc/database.org b/doc/database.org
new file mode 100644
index 00000000..6c079225
--- /dev/null
+++ b/doc/database.org
@@ -0,0 +1,245 @@
+- github Document reduction issue
+- github bio-vcf issue
+
+
+* GeneNetwork Database
+
+All *Data tables are large
+
+** User access
+
+GN1 uses access table and GN2 uses user table.
+
+** AvgMethod 
+
+Probesetfreeze refers to AvgMethod
+
+** BXDSnPosition
+
+Snp table (all snps)
+
+Mapping in GN1 shows snps when  you select a chromosome.
+
+** CaseAttribute(XRef)
+
+Metadata
+
+** CeleralINFO_mm6
+
+?
+
+** Chr_Length
+
+Default mm9, column for mm8
+
+** Dataset_mbat
+
+Menu for BXD (linkouts)
+
+** DatasetMapInvestigator
+
+Arthur?
+
+** DataSets
+
+Information/metadata
+
+** DatasetStatus
+
+Arthur private/public
+
+** DBList and DBType
+
+Hooked in API (URL encoding)
+
+** Docs
+
+GN2 only (see menu bar)
+
+** Ensembl* 
+
+Probe information
+
+(will be deprecated)
+
+** Genbank
+
+Linkout and not important
+
+** GeneCategory
+
+Not important. GeneWiki notes function classification.
+
+Deprecate.
+
+** GeneChip
+
+** GeneIDXRef
+
+Interspecies gene comparison
+
+** GeneList
+
+Track info
+
+** Genlist_rn3(3)
+
+Rat list
+
+** GeneMap_cuiyan
+
+Link outs
+
+** GeneRIF
+
+Wiki info (nightly updated from NCBI)
+
+XRef should be foreign keys
+
+** Geno
+
+SNP or marker info
+
+** GenoCode
+
+Belongs to someone else
+
+** GenoData
+
+Allele info
+
+** GenoFreeze
+
+Big menu (Freeze refers to menu)
+
+** GenoSE
+
+SE standard err, not used
+
+** GenoXREF
+
+Very important. Key links between Geno, GenoData
+
+** GORef
+
+GO terms
+
+** H2
+
+Heritability for probeset(?)
+
+** Homologene
+
+Homology, not used much
+
+** InbredSet
+
+Group in menu
+
+** Indelall, SnpAll, SnpPattern, SnpSource
+
+Indel Snp browser (variant browser Gn1)
+
+** Info*
+
+Infra system PhP 
+
+Data Info button 
+
+Infosystem users has separate entries
+
+Also Investigators, User, Organizations, 
+
+** LCorrRamin3 
+
+Lit. Correlations Prof. Ramin
+
+** Login
+
+GN2 login info
+
+** MachineAccessLog
+
+Old
+
+** MappingMethod
+
+GN1
+
+** News
+
+GN2
+
+** NStrain
+
+pheno           publishfreeze (menu)
+                       xref (keys)
+                          xref links to publish (pubmed), phenotype, pubishdata
+geno            genofreeze
+                       xref (keys)
+                          xref links to publish (pubmed), genotype, genodata
+probeset/expr.  probesetfreeze
+                       xref (keys)
+                          xref links to publish (pubmed), probeset, probesetdata
+probe/expr.  probefreeze
+                       xref (keys)
+                          xref links to publish (pubmed), probe, probedata
+
+Each dataset has 3 values (real value (1), number of samples (2), stderr (3))
+
+NStrain = number of phenotype samples
+
+ProbesetFreeze contains all data, incl. metabolomic.
+
+** Probe
+
+Probedata - main molecular data. Probesets, metabolome, 
+
+** Publication and publishdata (all pheno)
+
+Phenotype pubs
+
+** QuickSearch
+
+No longer used
+
+** role
+
+empty
+
+** Sample*
+
+No longer used
+
+** Species & Strain (should be sample)
+
+Menu
+
+** InbredSet 
+
+Menu
+
+** TableComments
+
+Metadata on DB
+
+** Temp*
+
+User upload data
+
+** Tissue
+
+Menu - 3rd level
+
+** TissueP*
+
+Correlation tables
+
+** User collection
+
+User selection - retained
+
+** UserPrivilege
+
+** Vlookup 
+