[pull] develop from solgenomics:master #29

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pull wants to merge 103 commits into Breeding-Insight:develop from solgenomics:master

.gitmodules

-Original file line number
+Diff line change
@@ Expand Up / @@ -99,13 +99,10 @@ @@
     	url = https://github.com/GMOD/chado_tools
     [submodule "cxgn/cxgn/Bio-Chado-Schema"]
     	path = cxgn/Bio-Chado-Schema
-    	url = https://github.com/GMOD/Bio-Chado-Schema
+    	url = https://github.com/solgenomics/bio-chado-schema
     [submodule "cxgn/chado_tools"]
     	path = cxgn/chado_tools
     	url = https://github.com/GMOD/chado_tools
-    [submodule "cxgn/Bio-Chado-Schema"]
-    	path = cxgn/Bio-Chado-Schema
-    	url = https://github.com/GMOD/Bio-Chado-Schema
     [submodule "cxgn/QuantGenResources"]
     	path = cxgn/QuantGenResources
     	url = https://github.com/solgenomics/QuantGenResources.git
@@ Expand All / @@ -117,3 +114,6 @@ @@
     	url = https://github.com/solgenomics/sgn-biotools.git
+    [submodule "cxgn/Bio-Chado-Schema"]
+    	path = cxgn/bio-chado-schema
+    	url = git@github.com:solgenomics/bio-chado-schema

Dockerfile

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -31,7 +31,7 @@ RUN bash -c "apt-key adv --keyserver keyserver.ubuntu.com --recv-key '95C0FAF38D
  
    # add cran backports repo and required deps

    #

    RUN echo "deb http://lib.stat.cmu.edu/R/CRAN/bin/linux/debian bullseye-cran40/" >> /etc/apt/sources.list

    RUN echo "deb https://cloud.r-project.org/bin/linux/debian/ bullseye-cran40/" >> /etc/apt/sources.list

    RUN echo "deb http://apt.postgresql.org/pub/repos/apt/ bullseye-pgdg main" | tee  /etc/apt/sources.list.d/pgdg.list

    @@ -42,7 +42,7 @@ RUN apt-get update --fix-missing -y
  
    RUN apt-get install -y aptitude

    RUN aptitude install -y npm libterm-readline-zoid-perl nginx starman emacs gedit vim less sudo htop git dkms linux-headers-generic perl-doc ack make xutils-dev nfs-common lynx xvfb ncbi-blast+ primer3 libmunge-dev libmunge2 munge slurm-wlm slurmctld slurmd libslurm-perl libssl-dev graphviz lsof imagemagick mrbayes muscle bowtie bowtie2 postfix mailutils libcupsimage2 postgresql-client-12 libglib2.0-dev libglib2.0-bin screen apt-transport-https libgdal-dev libproj-dev libudunits2-dev locales locales-all rsyslog cron libnlopt0 plink

    RUN aptitude install -y npm libimage-magick-perl libimage-exiftool-perl libterm-readline-zoid-perl nginx starman emacs gedit vim less sudo htop git dkms linux-headers-generic perl-doc ack make xutils-dev nfs-common lynx xvfb ncbi-blast+ primer3 libmunge-dev libmunge2 munge slurm-wlm slurmctld slurmd libslurm-perl libssl-dev graphviz lsof imagemagick mrbayes muscle clustalw bowtie bowtie2 postfix mailutils libcupsimage2 postgresql-client-12 libglib2.0-dev libglib2.0-bin screen apt-transport-https libgdal-dev libproj-dev libudunits2-dev locales locales-all rsyslog cron libnlopt0 plink

    # Set the locale correclty to UTF-8

    RUN locale-gen en_US.UTF-8

    @@ -92,11 +92,11 @@ RUN apt-get install libmoosex-runnable-perl -y
  
    RUN apt-get install libgdbm6 libgdm-dev -y

    RUN apt-get install nodejs -y

    RUN cpanm Selenium::Remote::Driver@1.44

    RUN cpanm Selenium::Remote::Driver@1.49

    #INSTALL OPENCV IMAGING LIBRARY

    RUN apt-get install -y python3-dev  python3-pip python3-numpy libgtk2.0-dev libgtk-3-0 libgtk-3-dev libavcodec-dev libavformat-dev libswscale-dev libhdf5-serial-dev libtbb2 libtbb-dev libjpeg-dev libpng-dev libtiff-dev libxvidcore-dev libatlas-base-dev gfortran libgdal-dev exiftool libzbar-dev cmake

    RUN apt-get install -y python3-dev  python3-pip python3-numpy libgtk2.0-dev libgtk-3-0 libgtk-3-dev libavcodec-dev libavformat-dev libswscale-dev libhdf5-serial-dev libtbb2 libtbb-dev libjpeg-dev libpng-dev libtiff-dev libxvidcore-dev libatlas-base-dev gfortran libgdal-dev exiftool libzbar-dev zbar-tools cmake

    RUN pip3 install --upgrade pip

    RUN pip3 install grpcio==1.40.0 imutils numpy matplotlib pillow statistics PyExifTool pytz pysolar scikit-image packaging pyzbar pandas opencv-python \

    @@ -134,7 +134,7 @@ RUN adduser --disabled-password --gecos "" -u 1250 production && chown -R produc
  
    WORKDIR /home/production/cxgn/sgn

    ENV PERL5LIB=/home/production/cxgn/Bio-Chado-Schema/lib:/home/production/cxgn/local-lib/:/home/production/cxgn/local-lib/lib/perl5:/home/production/cxgn/sgn/lib:/home/production/cxgn/cxgn-corelibs/lib:/home/production/cxgn/Phenome/lib:/home/production/cxgn/Cview/lib:/home/production/cxgn/ITAG/lib:/home/production/cxgn/biosource/lib:/home/production/cxgn/tomato_genome/lib:/home/production/cxgn/chado_tools/chado/lib:.

    ENV PERL5LIB=/home/production/cxgn/bio-chado-schema/lib:/home/production/cxgn/local-lib/:/home/production/cxgn/local-lib/lib/perl5:/home/production/cxgn/sgn/lib:/home/production/cxgn/cxgn-corelibs/lib:/home/production/cxgn/Phenome/lib:/home/production/cxgn/Cview/lib:/home/production/cxgn/ITAG/lib:/home/production/cxgn/biosource/lib:/home/production/cxgn/tomato_genome/lib:/home/production/cxgn/chado_tools/chado/lib:.

    ENV HOME=/home/production

    ENV PGPASSFILE=/home/production/.pgpass

    @@ -147,6 +147,9 @@ ARG CREATED
  
    ARG REVISION

    ARG BUILD_VERSION

    ENV VERSION=${BUILD_VERSION}

    ENV BUILD_DATE=${CREATED}

    LABEL maintainer="lam87@cornell.edu"

    LABEL org.opencontainers.image.created=$CREATED

    LABEL org.opencontainers.image.url="https://breedbase.org/"

    @@ -158,6 +161,8 @@ LABEL org.opencontainers.image.title="breedbase/breedbase"
  
    LABEL org.opencontainers.image.description="Breedbase web server"

    LABEL org.opencontainers.image.documentation="https://solgenomics.github.io/sgn/"

    # start services when running container...

    #

    ENTRYPOINT ["/entrypoint.sh"]

cxgn/Bio-Chado-Schema

Submodule Bio-Chado-Schema deleted from c86838

cxgn/Cview

Submodule Cview updated 1 files

+1 −1		lib/CXGN/Cview/Map/SGN/IL.pm

cxgn/R_libs

Submodule R_libs updated 1026 files

cxgn/bio-chado-schema

Submodule bio-chado-schema added at c9e3e9

cxgn/cassava

Submodule cassava updated 7 files

+3 −0		.gitignore
+25 −22		mason/site/footer/body.mas
+1 −0		mason/site/toolbar.mas
+17 −0		mason/site/toolbar/SOPs.mas
+2 −3		mason/site/toolbar/about.mas
+3 −0		mason/site/toolbar/analyze.mas
+2 −1		mason/site/toolbar/manage.mas

cxgn/cassbase

Submodule cassbase updated 20 files

+3 −0		README.md
+16,245 −0		cassava_trait.obo
+ −		img/CASS_Logo_black.png
+ −		img/CASS_Logo_white.png
+0 −440		mason/breeders_toolbox/trial/create_spreadsheet_dialog_and_create_postcomposed_traits_DEPRECATED.mas
+5 −3		mason/help/index.mas
+3 −3		mason/index.mas
+3 −9		mason/site/footer/body.mas
+4 −13		mason/site/toolbar/about.mas
+5 −3		mason/site/toolbar/analyze.mas
+1 −1		mason/site/toolbar/logo_and_name.mas
+11 −1		mason/site/toolbar/manage.mas
+1 −1		mason/site/toolbar/maps.mas
+3 −1		mason/site/toolbar/search_menu.mas
+0 −0		mason/stock/index.mas_old
+59 −59		ontology/cass_institute_ontology.obo
+5,948 −5,948		ontology/chebi_cass_with_missing5.obo
+126 −126		ontology/tissue_ontology.obo
+2,824 −3,276		ontology/tod_ontology.obo
+47 −47		ontology/unit_ontology.obo

cxgn/citrusgreening

Submodule citrusgreening updated 2 files

+108 −0		docker-compose.yml
+103 −0		sgn_local.conf

cxgn/cxgn-corelibs

Submodule cxgn-corelibs updated 3 files

+79 −4		lib/CXGN/Chado/Stock.pm
+82 −2		lib/CXGN/Image.pm
+436 −0		lib/CXGN/People/Schema/Result/SpJob.pm

cxgn/erysimum

Submodule erysimum updated 7 files

+2 −0		.gitignore
+37 −0		docker-compose.yml
+2 −6		mason/help/index.mas
+10 −0		mason/index.mas
+1 −1		mason/site/footer/body.mas
+0 −2		mason/site/toolbar/about.mas
+1 −1		mason/site/toolbar/genome_menu.mas

cxgn/fernbase

Submodule fernbase updated 1 files

+39 −0		docker-compose.yml

cxgn/gtsimsrch

Submodule gtsimsrch updated 99 files

+80 −0		README.md
+3 −0		big/cassava.dsgm
+3 −0		big/cassava.vcf
+3 −0		big/pedigree_table
+ −		cassava_dsout_agmr_histogram_480x360.png
+5,000 −0		data/5krandom_pedigrees
+8,170 −0		data/pedtable3col
+104 −47		include/gtset.h
+97 −54		include/pedigree.h
+23 −0		include/various.h
+53 −2		include/vect.h
+497 −0		lib/GD_plot.pm
+248 −0		lib/Gnuplot_plot.pm
+190 −0		lib/Hdata.pm
+815 −0		lib/Histograms.pm
+125 −0		lib/Plot.pm
+68 −0		moose/bin/analyze_ppout.pl
+156 −0		moose/bin/analyze_triples.pl
+42 −0		moose/bin/grandparents.pl
+527 −0		moose/bin/phased_parents.pl
+508 −0		moose/bin/phpars.pl
+53 −0		moose/bin/random_pedigrees.pl
+31 −0		moose/bin/sel_par_progs.pl
+222 −0		moose/bin/vcf2gts_phased.pl
+52 −0		moose/lib/Chromosome.pm
+74 −81		moose/lib/Cluster1d.pm
+32 −0		moose/lib/Marker.pm
+0 −0		other/compare_2file_agmrs.pl
+62 −0		other/dosage_matrix_info.pl
+57 −0		other/fix_pedigree_table.pl
+0 −0		other/nndists.pl
+44 −0		other/select_accessions_by_ids.pl
+102 −0		other/triples_3_cases.pl
+107 −0		other/uniquify_pedigree_file.pl
+80 −0		other/vcf_acc_subset.pl
+117 −0		other/vcf_format_check.pl
+0 −218		src/agmr_cluster.pl
+0 −69		src/best_triples.pl
+0 −30		src/bt_best_vs_nextbest.pl
+0 −97		src/bt_category_counts.pl
+0 −19		src/closest_pairs.pl
+503 −368		src/clusterer.pl
+0 −26		src/d_vs_md.pl
+0 −32		src/dosage_from_allele_depths.pl
+244 −100		src/duplicate_finder.pl
+671 −316		src/duplicate_search.c
+568 −160		src/find_parents.c
+1,291 −415		src/gtset.c
+92 −0		src/gwas/Manhattan.pl
+48 −0		src/gwas/dsgs2ped.pl
+46 −0		src/gwas/fn_vs_fp.pl
+43 −0		src/gwas/manhattan.gnuplot
+2 −2		src/gwas/plnkout2dsout.pl
+238 −0		src/gwas/rand_dupe_no_dupe.pl
+115 −0		src/gwas/sim_gwas_dupes_vs_nodupes.pl
+154 −0		src/gwas/simmultiphenotypes.pl
+212 −0		src/histogram.pl
+0 −66		src/maf_freqs.pl
+15 −14		src/makefile
+0 −48		src/multipedigrees.pl
+0 −102		src/n01_3etc.pl
+0 −137		src/nxy_z.pl
+271 −0		src/old/DSvcf2gts.pl
+0 −0		src/old/bad_accessions_begone.pl
+1 −1		src/old/find_parent_candidates.c
+75 −113		src/old/pedigree_test.c
+171 −0		src/old/plnkout_to_dsout.c
+4 −4		src/old/remove_duplicates.pl
+70 −57		src/old/vcf2gts.pl
+646 −1,208		src/pedigree.c
+0 −12		src/pedigree_ids.pl
+0 −70		src/progeny_parents_both.pl
+0 −208		src/pt_vs_fp.pl
+0 −75		src/ptfpbt.pl
+0 −30		src/select_accessions_by_ids.pl
+0 −87		src/triples_3_cases.pl
+229 −199		src/uniquify.pl
+0 −54		src/uniquify_pedigree_file.pl
+44 −1		src/various.c
+0 −17		src/vcf_data.pl
+92 −0		src/vcf_thru_find_parents.pl
+979 −0		src/vcf_to_dsgm.c
+0 −514		src/vcf_to_gts.c
+164 −17		src/vect.c
+0 −13		src/xvcf.pl
+7,628 −0		testing/alt0.fpout_std
+8,114 −0		testing/alt1.fpout_std
+7,628 −0		testing/alt2.fpout_std
+8,114 −0		testing/alt3.fpout_std
+38 −0		testing/dstest.pl
+109 −0		testing/fpout_compare.pl
+8,117 −0		testing/noped.fpout_std
+112 −0		testing/test_find_parents.pl
+59 −0		util/quadrants.pl
+16 −0		util/sel_columns.pl
+37 −0		util/select_random_columns.pl
+19 −0		util/sort_by_col.pl
+73 −0		util/venn_lines.pl
+53 −0		util/words_per_line.pl

cxgn/local-lib

Submodule local-lib updated 722 files

cxgn/musabase

Submodule musabase updated 9 files

+3 −0		mason/index.mas
+4 −0		mason/pages/NARITA_pathology_results.mas
+24 −11		mason/site/footer/body.mas
+1 −0		mason/site/toolbar/analyze.mas
+9 −6		mason/site/toolbar/manage.mas
+2 −2		mason/site/toolbar/maps.mas
+1 −1		mason/site/toolbar/pathogens.mas
+1 −0		mason/site/toolbar/search_menu.mas
+7 −3		mason/site/toolbar/sops.mas

cxgn/sgn

Submodule sgn updated 1679 files

cxgn/solgenomics

Submodule solgenomics updated 13 files

+2 −0		.gitignore
+18 −0		crontab
+44 −0		docker-compose.yml
+34 −3		mason/genomes/Solanum_tuberosum.mas
+10 −53		mason/index.mas
+40 −0		mason/projects/Solanum_pan_genomics.mas
+28 −0		mason/projects/TomDel.mas
+110 −0		mason/projects/eggplant_pan_genomics.mas
+13 −9		mason/site/footer/body.mas
+12 −10		mason/site/header/analytics.mas
+2 −0		mason/site/toolbar/projects.mas
+1 −0		mason/site/toolbar/search_menu.mas
+5 −2		mason/site/toolbar/tools.mas

cxgn/sweetpotatobase

Submodule sweetpotatobase updated 5 files

+2 −0		.gitignore
+35 −0		docker-compose.yml
+22 −16		mason/site/footer/body.mas
+29 −7		mason/site/toolbar/analyze.mas
+1 −0		mason/site/toolbar/manage.mas

cxgn/yambase

Submodule yambase updated 4 files

+2 −0		.gitignore
+0 −5		mason/index.mas
+36 −70		mason/site/footer/body.mas
+0 −103		sgn_local.conf

docker-compose.override.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -11,6 +11,7 @@ services: @@
           - type: bind
             source: .git
             target: /home/production/.git
+          - shared_data:/downloads
         environment:
           MODE: 'DEVELOPMENT'
           PGDATABASE: breedbase
@@ Expand All / @@ -19,14 +20,15 @@ services: @@
           PGUSER: postgres
           SGN_TEST_SERVER: http://breedbase:3010
           SGN_REMOTE_SERVER_ADDR: selenium
+          DBIC_TRACE: 0
       selenium:
         container_name: selenium
         image: selenium/standalone-firefox-debug
         volumes:
           - type: bind
             source: ./cxgn/sgn/t/data
             target: /home/production/cxgn/sgn/t/data
+          - shared_data:/downloads
         ports:
           - 5900:5900
           - 4444:4444
@@ Expand All / @@ -35,3 +37,6 @@ services: @@
         environment:
           POSTGRES_DB: breedbase
           POSTGRES_PASSWORD: postgres
+    volumes:
+      shared_data:

docker-compose.test.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -3,7 +3,7 @@ services: @@
         build:
           context: .
           cache_from:
-            - breedbase/breedbase:v0.54
+            - breedbase/breedbase:latest
         environment:
           HOME: /root
           MODE: 'TESTING'
@@ Expand All / @@ -19,6 +19,7 @@ services: @@
           - ./cxgn:/home/production/cxgn
           # repos/sgn/sgn_test.conf assumes /home/vagrant
           - ./.git:/home/production/.git
+          - shared_data:/downloads
         command: ["t/unit", "t/unit_fixture", "t/unit_mech"]
         networks:
           - test-breedbase
@@ Expand All / @@ -34,6 +35,7 @@ services: @@
           - type: bind
             source: ./cxgn/sgn/t/data
             target: /home/production/cxgn/sgn/t/data
+          - shared_data:/downloads
         ports:
            - 5900:5900
            - 4444:4444
@@ Expand All / @@ -49,5 +51,8 @@ services: @@
         networks:
           - test-breedbase
+    volumes:
+      shared_data:
     networks:
       test-breedbase:

docker-compose.yml

-Original file line number
+Diff line change
@@ Expand Up / @@ -4,7 +4,6 @@ services: @@
           - webdata:/home/production/volume
         ports:
           - 8080:8080
-          - 25:25
         image: breedbase/breedbase:latest
         depends_on:
           - breedbase_db
@@ Expand Down @@

entrypoint.sh

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -8,6 +8,8 @@ chown 106 /etc/munge/munge.key
  
    /etc/init.d/slurmd start

    #/etc/init.d/postgres start

    chown root /etc/crontab # in case it was mounted from local dir

    if [ "${MODE}" = 'TESTING' ]; then

        exec perl t/test_fixture.pl --carpalways -v "${@}"

    fi

    @@ -18,7 +20,7 @@ umask 002
  
    echo "CHECKING IF A DATABASE NEEDS TO BE INSTALLED...";

    if [ $(psql -h ${PGHOST} -U postgres -d postgres -Atc 'select count(distinct table_schema) from information_schema.tables;') == "2" ]; then

    if [[ $(psql -lqt -h ${PGHOST} -U ${PGUSER}  | cut -d '|' -f1  | sed 's/^[[:blank:]]*//;s/[[:blank:]]*$//;' |  grep -w breedbase ) = '' ]]; then

        echo "INSTALLING DATABASE...";

        echo "CREATING web_usr...";

        psql -d postgres -c "CREATE USER web_usr PASSWORD 'postgres';"

    @@ -116,3 +118,8 @@ else
  
      chmod 777 /var/log/sgn/error.log

      tail -f /var/log/sgn/error.log

    fi

    # for unigene page, compile drawcontig align program

    #cd /home/production/cxgn/sgn/programs

    #make

    #cd /home/production/cxgn/sgn

starmachine.conf

-Original file line number
+Diff line change
@@ Expand Up / @@ -2,7 +2,7 @@ root_dir = /home/production/cxgn/starmachine @@
     env[CATALYST_CONFIG] = /etc/starmachine
-    env[PERL5LIB] = /home/production/cxgn/biosource/lib:/home/production/cxgn/sgn/lib:/home/production/cxgn/cxgn-corelibs/lib:/home/production/cxgn/tomato_genome/lib:/home/production/cxgn/ITAG/lib:/home/production/cxgn/Cview/lib:/home/production/cxgn/Phenome/lib:/home/production/cxgn/local-lib/lib:/home/production/cxgn/local-lib/lib/perl5:/home/production/cxgn/local-lib/bin
+    env[PERL5LIB] = /home/production/cxgn/bio-chado-schema/lib:/home/production/cxgn/biosource/lib:/home/production/cxgn/sgn/lib:/home/production/cxgn/cxgn-corelibs/lib:/home/production/cxgn/tomato_genome/lib:/home/production/cxgn/ITAG/lib:/home/production/cxgn/Cview/lib:/home/production/cxgn/Phenome/lib:/home/production/cxgn/local-lib/lib:/home/production/cxgn/local-lib/lib/perl5:/home/production/cxgn/local-lib/bin
     sgn[env][CATALYST_CONFIG] = /home/production/cxgn/sgn/sgn.conf
     sgn[app_dir] = /home/production/cxgn/sgn
     sgn[psgi_file] = bin/sgn.psgi
@@ Expand Down @@

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