Merge branch 'master' of github.com:genenetwork/genenetwork2 into development

Conflicts:
	.gitignore

15 files changed, 340 insertions, 5 deletions

diff --git a/.gitignore b/.gitignore
index 15c0c848..51aaabbb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,4 +7,8 @@
 web/new_genotypes/HSNIH.json
 wqflask/secure_server.py
 wqflask/base/webqtlConfig.py
-wqflask/wqflask/static/output/*
+build/
+dist/
+*.egg-info/
+EGG-INFO/
+wqflask/output/*
diff --git a/MANIFEST.in b/MANIFEST.in
new file mode 100644
index 00000000..f4ea2316
--- /dev/null
+++ b/MANIFEST.in
@@ -0,0 +1,262 @@
+include wqflask/*
+include wqflask/other_config/*
+include wqflask/other_config/nginx_conf/*
+include wqflask/cfg/*
+include wqflask/maintenance/*
+include wqflask/maintenance/dataset/*
+include wqflask/maintenance/dataset/datasampledir/*
+include wqflask/maintenance/dataset/datasampledir/load_phenotypes/*
+include wqflask/maintenance/dataset/datasampledir/load_genotypes/*
+include wqflask/utility/*
+include wqflask/wqflask/*
+include wqflask/wqflask/templates/*
+include wqflask/wqflask/templates/admin/*
+include wqflask/wqflask/templates/email/*
+include wqflask/wqflask/templates/collections/*
+include wqflask/wqflask/templates/new_security/*
+include wqflask/wqflask/correlation/*
+include wqflask/wqflask/interval_mapping/*
+include wqflask/wqflask/interval_analyst/*
+include wqflask/wqflask/my_pylmm/*
+include wqflask/wqflask/my_pylmm/scripts/*
+include wqflask/wqflask/my_pylmm/pyLMM/*
+include wqflask/wqflask/my_pylmm/data/*
+include wqflask/wqflask/static/*
+include wqflask/wqflask/static/dbdoc/*
+include wqflask/wqflask/static/new/*
+include wqflask/wqflask/static/new/js_external/*
+include wqflask/wqflask/static/new/js_external/zxcvbn/*
+include wqflask/wqflask/static/new/css/*
+include wqflask/wqflask/static/new/javascript/*
+include wqflask/wqflask/static/new/javascript/node_modules/*
+include wqflask/wqflask/static/new/javascript/node_modules/.bin/*
+include wqflask/wqflask/static/new/packages/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/dist/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/lib/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/localization/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/demo/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/demo/marketo/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/demo/marketo/images/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/demo/captcha/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/demo/captcha/fonts/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/demo/captcha/images/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/demo/images/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/demo/tabs/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/demo/js/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/demo/login/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/demo/login/images/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/demo/css/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/demo/milk/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/demo/multipart/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/demo/multipart/js/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/demo/tinymce/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/demo/tinymce/themes/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/demo/tinymce/themes/simple/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/demo/tinymce/themes/simple/img/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/demo/tinymce/themes/simple/langs/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/demo/tinymce/themes/simple/skins/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/demo/tinymce/themes/simple/skins/default/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/test/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/test/qunit/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/test/selects/*
+include wqflask/wqflask/static/new/packages/ValidationPlugin/test/firebug/*
+include wqflask/wqflask/static/new/packages/nvd3/*
+include wqflask/wqflask/static/new/packages/noUiSlider/*
+include wqflask/wqflask/static/new/packages/DataTables/*
+include wqflask/wqflask/static/new/packages/DataTables/images/*
+include wqflask/wqflask/static/new/packages/DataTables/js/*
+include wqflask/wqflask/static/new/packages/DataTables/css/*
+include wqflask/wqflask/static/new/packages/DataTables/src/*
+include wqflask/wqflask/static/new/packages/DataTables/src/api/*
+include wqflask/wqflask/static/new/packages/DataTables/src/core/*
+include wqflask/wqflask/static/new/packages/DataTables/src/ext/*
+include wqflask/wqflask/static/new/packages/DataTables/src/model/*
+include wqflask/wqflask/static/new/packages/DataTables/extensions/*
+include wqflask/wqflask/static/new/packages/DataTables/unit_testing/*
+include wqflask/wqflask/static/new/packages/DataTables/unit_testing/templates/*
+include wqflask/wqflask/static/new/packages/DataTables/unit_testing/performance/*
+include wqflask/wqflask/static/new/packages/DataTables/unit_testing/tests/*
+include wqflask/wqflask/static/new/packages/DataTables/unit_testing/tests/1_dom/*
+include wqflask/wqflask/static/new/packages/DataTables/unit_testing/tests_onhold/*
+include wqflask/wqflask/static/new/packages/DataTables/unit_testing/tests_onhold/5_ajax_objects/*
+include wqflask/wqflask/static/new/packages/DataTables/unit_testing/tests_onhold/3_ajax/*
+include wqflask/wqflask/static/new/packages/DataTables/unit_testing/tests_onhold/2_js/*
+include wqflask/wqflask/static/new/packages/DataTables/unit_testing/tests_onhold/4_server-side/*
+include wqflask/wqflask/static/new/packages/DataTables/unit_testing/tests_onhold/6_delayed_rendering/*
+include wqflask/wqflask/static/new/packages/DataTables/unit_testing/tests_onhold/1_dom/*
+include wqflask/wqflask/static/packages/*
+include wqflask/wqflask/static/packages/TableTools/*
+include wqflask/wqflask/static/packages/TableTools/media/*
+include wqflask/wqflask/static/packages/TableTools/media/images/*
+include wqflask/wqflask/static/packages/TableTools/media/images/psd/*
+include wqflask/wqflask/static/packages/TableTools/media/swf/*
+include wqflask/wqflask/static/packages/TableTools/media/js/*
+include wqflask/wqflask/static/packages/TableTools/media/css/*
+include wqflask/wqflask/static/packages/TableTools/media/as3/*
+include wqflask/wqflask/static/packages/TableTools/media/as3/lib/*
+include wqflask/wqflask/static/packages/underscore/*
+include wqflask/wqflask/static/packages/bootstrap/*
+include wqflask/wqflask/static/packages/bootstrap/fonts/*
+include wqflask/wqflask/static/packages/bootstrap/js/*
+include wqflask/wqflask/static/packages/bootstrap/css/*
+include wqflask/wqflask/static/packages/bootstrap/img/*
+include wqflask/wqflask/static/packages/novus-nvd3-d51729c/*
+include wqflask/wqflask/static/packages/novus-nvd3-d51729c/lib/*
+include wqflask/wqflask/static/packages/novus-nvd3-d51729c/deprecated/*
+include wqflask/wqflask/static/packages/novus-nvd3-d51729c/deprecated/charts/*
+include wqflask/wqflask/static/packages/novus-nvd3-d51729c/test/*
+include wqflask/wqflask/static/packages/novus-nvd3-d51729c/src/*
+include wqflask/wqflask/static/packages/novus-nvd3-d51729c/src/models/*
+include wqflask/wqflask/static/packages/novus-nvd3-d51729c/src/models/backup/*
+include wqflask/wqflask/static/packages/novus-nvd3-d51729c/examples/*
+include wqflask/wqflask/static/packages/novus-nvd3-d51729c/examples/images/*
+include wqflask/wqflask/static/packages/DT_bootstrap/*
+include wqflask/wqflask/static/packages/ckeditor/*
+include wqflask/wqflask/static/packages/ckeditor/lang/*
+include wqflask/wqflask/static/packages/ckeditor/adapters/*
+include wqflask/wqflask/static/packages/ckeditor/skins/*
+include wqflask/wqflask/static/packages/ckeditor/skins/moono/*
+include wqflask/wqflask/static/packages/ckeditor/skins/moono/images/*
+include wqflask/wqflask/static/packages/ckeditor/skins/moono/images/hidpi/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/div/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/div/dialogs/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/a11yhelp/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/a11yhelp/dialogs/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/a11yhelp/dialogs/lang/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/templates/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/templates/templates/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/templates/templates/images/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/templates/dialogs/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/find/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/find/dialogs/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/scayt/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/scayt/dialogs/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/dialog/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/flash/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/flash/dialogs/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/flash/images/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/about/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/about/dialogs/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/about/dialogs/hidpi/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/pastefromword/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/pastefromword/filter/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/specialchar/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/specialchar/dialogs/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/specialchar/dialogs/lang/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/wsc/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/wsc/dialogs/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/forms/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/forms/dialogs/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/forms/images/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/link/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/link/dialogs/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/link/images/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/link/images/hidpi/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/iframe/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/iframe/dialogs/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/iframe/images/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/colordialog/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/colordialog/dialogs/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/table/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/table/dialogs/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/smiley/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/smiley/dialogs/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/smiley/images/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/liststyle/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/liststyle/dialogs/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/clipboard/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/clipboard/dialogs/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/showblocks/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/showblocks/images/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/pagebreak/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/pagebreak/images/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/magicline/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/magicline/images/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/magicline/images/hidpi/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/preview/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/image/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/image/dialogs/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/image/images/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/tabletools/*
+include wqflask/wqflask/static/packages/ckeditor/plugins/tabletools/dialogs/*
+include wqflask/wqflask/static/packages/ckeditor/samples/*
+include wqflask/wqflask/static/packages/ckeditor/samples/assets/*
+include wqflask/wqflask/static/packages/ckeditor/samples/assets/uilanguages/*
+include wqflask/wqflask/static/packages/ckeditor/samples/assets/outputxhtml/*
+include wqflask/wqflask/static/packages/ckeditor/samples/assets/inlineall/*
+include wqflask/wqflask/static/packages/ckeditor/samples/plugins/*
+include wqflask/wqflask/static/packages/ckeditor/samples/plugins/dialog/*
+include wqflask/wqflask/static/packages/ckeditor/samples/plugins/dialog/assets/*
+include wqflask/wqflask/static/packages/ckeditor/samples/plugins/enterkey/*
+include wqflask/wqflask/static/packages/ckeditor/samples/plugins/toolbar/*
+include wqflask/wqflask/static/packages/ckeditor/samples/plugins/magicline/*
+include wqflask/wqflask/static/packages/ckeditor/samples/plugins/htmlwriter/*
+include wqflask/wqflask/static/packages/ckeditor/samples/plugins/htmlwriter/assets/*
+include wqflask/wqflask/static/packages/ckeditor/samples/plugins/htmlwriter/assets/outputforflash/*
+include wqflask/wqflask/static/packages/ckeditor/samples/plugins/wysiwygarea/*
+include wqflask/wqflask/static/packages/colorbox/*
+include wqflask/wqflask/static/packages/colorbox/example5/*
+include wqflask/wqflask/static/packages/colorbox/example5/images/*
+include wqflask/wqflask/static/packages/colorbox/example4/*
+include wqflask/wqflask/static/packages/colorbox/example4/images/*
+include wqflask/wqflask/static/packages/colorbox/example1/*
+include wqflask/wqflask/static/packages/colorbox/example1/images/*
+include wqflask/wqflask/static/packages/colorbox/content/*
+include wqflask/wqflask/static/packages/colorbox/example3/*
+include wqflask/wqflask/static/packages/colorbox/example3/images/*
+include wqflask/wqflask/static/packages/colorbox/example2/*
+include wqflask/wqflask/static/packages/colorbox/example2/images/*
+include wqflask/wqflask/static/packages/colorbox/i18n/*
+include wqflask/wqflask/static/packages/node/*
+include wqflask/wqflask/static/packages/node/tools/*
+include wqflask/wqflask/static/packages/node/tools/closure_linter/*
+include wqflask/wqflask/static/packages/bootstrap-old/*
+include wqflask/wqflask/static/packages/bootstrap-old/js/*
+include wqflask/wqflask/static/packages/bootstrap-old/css/*
+include wqflask/wqflask/static/packages/bootstrap-old/img/*
+include wqflask/wqflask/static/packages/pragmaticly-smart-time-ago-40fa376/*
+include wqflask/wqflask/static/packages/pragmaticly-smart-time-ago-40fa376/lib/*
+include wqflask/wqflask/static/packages/pragmaticly-smart-time-ago-40fa376/lib/locales/*
+include wqflask/wqflask/static/packages/pragmaticly-smart-time-ago-40fa376/test/*
+include wqflask/wqflask/static/packages/pragmaticly-smart-time-ago-40fa376/test/lib/*
+include wqflask/wqflask/static/packages/pragmaticly-smart-time-ago-40fa376/test/specs/*
+include wqflask/wqflask/static/packages/pragmaticly-smart-time-ago-40fa376/src/*
+include wqflask/wqflask/static/packages/pragmaticly-smart-time-ago-40fa376/src/locales/*
+include wqflask/wqflask/static/packages/jqplot/*
+include wqflask/wqflask/static/packages/jqplot/docs/*
+include wqflask/wqflask/static/packages/jqplot/docs/index/*
+include wqflask/wqflask/static/packages/jqplot/docs/styles/*
+include wqflask/wqflask/static/packages/jqplot/docs/files/*
+include wqflask/wqflask/static/packages/jqplot/docs/files/images/*
+include wqflask/wqflask/static/packages/jqplot/docs/files/plugins/*
+include wqflask/wqflask/static/packages/jqplot/docs/search/*
+include wqflask/wqflask/static/packages/jqplot/docs/javascript/*
+include wqflask/wqflask/static/packages/jqplot/examples/*
+include wqflask/wqflask/static/packages/jqplot/examples/colorpicker/*
+include wqflask/wqflask/static/packages/jqplot/examples/colorpicker/images/*
+include wqflask/wqflask/static/packages/jqplot/examples/images/*
+include wqflask/wqflask/static/packages/jqplot/examples/jquery-ui/*
+include wqflask/wqflask/static/packages/jqplot/examples/jquery-ui/js/*
+include wqflask/wqflask/static/packages/jqplot/examples/jquery-ui/css/*
+include wqflask/wqflask/static/packages/jqplot/examples/jquery-ui/css/smoothness/*
+include wqflask/wqflask/static/packages/jqplot/examples/jquery-ui/css/smoothness/images/*
+include wqflask/wqflask/static/packages/jqplot/examples/jquery-ui/css/ui-lightness/*
+include wqflask/wqflask/static/packages/jqplot/examples/jquery-ui/css/ui-lightness/images/*
+include wqflask/wqflask/static/packages/jqplot/examples/syntaxhighlighter/*
+include wqflask/wqflask/static/packages/jqplot/examples/syntaxhighlighter/scripts/*
+include wqflask/wqflask/static/packages/jqplot/examples/syntaxhighlighter/styles/*
+include wqflask/wqflask/static/packages/jqplot/plugins/*
+include wqflask/wqflask/correlation_matrix/*
+include wqflask/wqflask/show_trait/*
+include wqflask/wqflask/wgcna/*
+include wqflask/wqflask/marker_regression/*
+include wqflask/wqflask/heatmap/*
+include wqflask/flask_security/*
+include wqflask/flask_security/templates/*
+include wqflask/flask_security/templates/security/*
+include wqflask/flask_security/templates/security/email/*
+include wqflask/dbFunction/*
+include wqflask/basicStatistics/*
+include wqflask/base/*
diff --git a/doc/GUIX-Reproducible-from-source.org b/doc/GUIX-Reproducible-from-source.org
new file mode 100644
index 00000000..b88eb9e8
--- /dev/null
+++ b/doc/GUIX-Reproducible-from-source.org
@@ -0,0 +1,35 @@
+#+TITLE: Installing GeneNetwork services with GNU Guix
+
+* Table of Contents                                                     :TOC:
+ - [[#introduction][Introduction]]
+ - [[#binary-deployment][Binary deployment]]
+ - [[#from-source-deployment][From source deployment]]
+
+* Introduction
+
+Large system deployments tend to get very complex. In this document we
+explain the GeneNetwork deployment system which is based on GNU Guix
+(see Pjotr's [[https://github.com/pjotrp/guix-notes/blob/master/README.md][Guix-notes]]).
+
+* Binary deployment
+
+NYA (will go to README)
+
+* From source deployment
+
+GNU Guix allows for [[https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org][reproducible deployment]] based on a checked out
+Guix repository - use gn-stable for that:
+
+#+begin_src sh   :lang bash
+mkdir genenetwork
+cd genenetwork
+git checkout https://github.com/genenetwork/guix.git gn-stable-guix
+git checkout https://github.com/genenetwork/guix-bioinformatics.git
+#+end_src
+
+Next build guix (and run) following the instructions in [[https://github.com/pjotrp/guix-notes/blob/master/INSTALL.org#building-gnu-guix-from-source-using-guix][guix-notes]].
+
+Once that is done we can add the guix-bioinformatics path with
+
+: env GUIX_PACKAGE_PATH=../guix-bioinformatics ./pre-inst-env guix package -A slurm
+
diff --git a/doc/README.org b/doc/README.org
new file mode 100644
index 00000000..f6ab6a52
--- /dev/null
+++ b/doc/README.org
@@ -0,0 +1,28 @@
+#+TITLE: Installing GeneNetwork services with GNU Guix
+
+* Table of Contents                                                     :TOC:
+ - [[#introduction][Introduction]]
+ - [[#binary-deployment][Binary deployment]]
+ - [[#from-source-deployment][From source deployment]]
+
+* Introduction
+
+Large system deployments tend to get very complex. In this document we
+explain the GeneNetwork deployment system which is based on GNU Guix
+(see Pjotr's [[https://github.com/pjotrp/guix-notes/blob/master/README.md][Guix-notes]]).
+
+* Binary deployment
+
+NYA
+
+* From source deployment
+
+GNU Guix allows for [[https://github.com/pjotrp/guix-notes/blob/master/REPRODUCIBLE.org][reproducible deployment]] based on a checked out
+Guix repository - use gn-stable for that:
+
+#+begin_src sh   :lang bash
+mkdir genenetwork
+cd genenetwork
+git checkout https://github.com/genenetwork/guix.git gn-stable-guix
+git checkout https://github.com/genenetwork/guix-bioinformatics.git
+#+end_src
diff --git a/misc/gn_installation_notes.txt b/doc/gn_installation_notes.txt
index 584080f7..584080f7 100644
--- a/misc/gn_installation_notes.txt
+++ b/doc/gn_installation_notes.txt
diff --git a/misc/new_variable_names.txt b/doc/new_variable_names.txt
index c11c160e..c11c160e 100644
--- a/misc/new_variable_names.txt
+++ b/doc/new_variable_names.txt
diff --git a/misc/notes.txt b/doc/notes.txt
index f8ce2759..f8ce2759 100644
--- a/misc/notes.txt
+++ b/doc/notes.txt
diff --git a/misc/notes_DA.txt b/doc/notes_DA.txt
index 410e0182..410e0182 100644
--- a/misc/notes_DA.txt
+++ b/doc/notes_DA.txt
diff --git a/misc/requirements.txt b/doc/requirements.txt
index 39ee5652..39ee5652 100644
--- a/misc/requirements.txt
+++ b/doc/requirements.txt
diff --git a/misc/todo.txt b/doc/todo.txt
index 1d781b13..1d781b13 100644
--- a/misc/todo.txt
+++ b/doc/todo.txt
diff --git a/genotype_files/genotypes/.gitattributes b/genotype_files/genotypes/.gitattributes
deleted file mode 100644
index c311ac85..00000000
--- a/genotype_files/genotypes/.gitattributes
+++ /dev/null
@@ -1 +0,0 @@
-*.geno filter=lfs -crlf
diff --git a/genotype_files/new_genotypes/.gitattributes b/genotype_files/new_genotypes/.gitattributes
deleted file mode 100644
index 912ed80c..00000000
--- a/genotype_files/new_genotypes/.gitattributes
+++ /dev/null
@@ -1 +0,0 @@
-*.json filter=lfs -crlf
diff --git a/setup.py b/setup.py
new file mode 100755
index 00000000..1b11acc0
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,8 @@
+from setuptools import setup, find_packages
+
+setup(name='genenetwork2',
+      version='2.0',
+      include_package_data=True,
+      # packages=find_packages()
+      packages=['wqflask']
+      )
diff --git a/wqflask/__init__.py b/wqflask/__init__.py
new file mode 100644
index 00000000..4aa081d3
--- /dev/null
+++ b/wqflask/__init__.py
@@ -0,0 +1,2 @@
+import logging
+from wqflask import app
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index 68cc8b18..a7edbc48 100755
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -72,7 +72,6 @@
                 </select>
             </div>
         </div>
-        {% if this_trait.dataset.type == 'ProbeSet' %}
         <div class="form-group">
             <label class="col-xs-1 control-label">Min Expr</label>
             <div class="col-xs-2 controls">
@@ -89,7 +88,6 @@
                 <br>
             </div>
         </div>
-        {% endif %}
         <div class="form-group">
             <label class="col-xs-1 control-label">Range</label>
             <div class="col-xs-3 controls">