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| # Auto detect text files and perform LF normalization | ||
| * text=auto | ||
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| # Custom for Visual Studio | ||
| *.cs diff=csharp | ||
| *.sln merge=union | ||
| *.csproj merge=union | ||
| *.vbproj merge=union | ||
| *.fsproj merge=union | ||
| *.dbproj merge=union | ||
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| # Standard to msysgit | ||
| *.doc diff=astextplain | ||
| *.DOC diff=astextplain | ||
| *.docx diff=astextplain | ||
| *.DOCX diff=astextplain | ||
| *.dot diff=astextplain | ||
| *.DOT diff=astextplain | ||
| *.pdf diff=astextplain | ||
| *.PDF diff=astextplain | ||
| *.rtf diff=astextplain | ||
| *.RTF diff=astextplain |
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| #!/bin/bash | ||
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| check_errs() | ||
| { | ||
| # Function. Parameter 1 is the return code | ||
| # Para. 2 is text to display on failure. | ||
| if [ "${1}" -ne "0" ]; then | ||
| echo "ERROR: ${1} : ${2}" | ||
| exit ${1} | ||
| fi | ||
| } | ||
| PGUSER=devlincsweb | ||
| DATADIR=/groups/pharmacoresponse/data/dev | ||
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| #/home/sde4/sql/drop-all.pl devlincs | ||
| ./generate_drop_all.sh devlincsweb devlincs dev.pgsql.orchestra | psql -Udevlincsweb devlincs -h dev.pgsql.orchestra | ||
| check_errs $? "dropdb fails" | ||
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| source /www/dev.lincs.hms.harvard.edu/support/virtualenv/bin/activate | ||
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| django/manage.py syncdb | ||
| check_errs $? "syncdb fails" | ||
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| echo 'import cell table ...' | ||
| python src/populate_cell.py sampledata/LINCS_Cells_20120727.xls 'HMS-LINCS cell line metadata' | ||
| check_errs $? "populate cell fails" | ||
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| echo 'import small molecule...' | ||
| python src/populate_smallmolecule.py $DATADIR/HMS_LINCS-1.sdf | ||
| check_errs $? "import sdf fails" | ||
| python src/populate_smallmolecule.py $DATADIR/HMS_LINCS-2.sdf | ||
| check_errs $? "import sdf fails" | ||
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| echo 'import kinases...' | ||
| python src/import_protein.py -f sampledata/HMS-LINCS_KinaseReagents_MetaData_20120906_DRAFT.xls | ||
| check_errs $? 'import kinases fails' | ||
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| echo 'import screen results...' | ||
| python src/import_dataset.py -f sampledata/moerke_2color_IA-LM.xls | ||
| check_errs $? "import dataset fails" | ||
| python src/import_dataset.py -f sampledata/tang_MitoApop2_5637.xls | ||
| check_errs $? "import dataset result fails" | ||
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| echo 'import studies' | ||
| python ./src/import_dataset.py -f sampledata/Study300002_HMSL10008_sorafenib_ambit.xls | ||
| check_errs $? "import study dataset fails" | ||
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| python src/import_libraries.py -f sampledata/libraries.xls | ||
| check_errs $? "import library fails" | ||
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| python src/create_indexes.py | psql -U devlincsweb devlincs -h dev.pgsql.orchestra -v ON_ERROR_STOP=1 | ||
| #check_errs $? "create indexes fails" | ||
| #!/bin/bash | ||
|
|
||
| check_errs() | ||
| { | ||
| # Function. Parameter 1 is the return code | ||
| # Para. 2 is text to display on failure. | ||
| if [ "${1}" -ne "0" ]; then | ||
| echo "ERROR: ${1} : ${2}" | ||
| exit ${1} | ||
| fi | ||
| } | ||
| PGUSER=devlincsweb | ||
| DATADIR=/groups/pharmacoresponse/data/dev | ||
|
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| #/home/sde4/sql/drop-all.pl devlincs | ||
| ./generate_drop_all.sh devlincsweb devlincs dev.pgsql.orchestra | psql -Udevlincsweb devlincs -h dev.pgsql.orchestra | ||
| check_errs $? "dropdb fails" | ||
|
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| source /www/dev.lincs.hms.harvard.edu/support/virtualenv/bin/activate | ||
|
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||
| django/manage.py syncdb | ||
| check_errs $? "syncdb fails" | ||
|
|
||
| echo 'import cell table ...' | ||
| python src/populate_cell.py sampledata/LINCS_Cells_20120727.xls 'HMS-LINCS cell line metadata' | ||
| check_errs $? "populate cell fails" | ||
|
|
||
| echo 'import small molecule...' | ||
| python src/populate_smallmolecule.py $DATADIR/HMS_LINCS-1.sdf | ||
| check_errs $? "import sdf fails" | ||
| python src/populate_smallmolecule.py $DATADIR/HMS_LINCS-2.sdf | ||
| check_errs $? "import sdf fails" | ||
|
|
||
| echo 'import kinases...' | ||
| python src/import_protein.py -f sampledata/HMS-LINCS_KinaseReagents_MetaData_20120906_DRAFT.xls | ||
| check_errs $? 'import kinases fails' | ||
|
|
||
| echo 'import screen results...' | ||
| python src/import_dataset.py -f sampledata/moerke_2color_IA-LM.xls | ||
| check_errs $? "import dataset fails" | ||
| python src/import_dataset.py -f sampledata/tang_MitoApop2_5637.xls | ||
| check_errs $? "import dataset result fails" | ||
|
|
||
| echo 'import studies' | ||
| python ./src/import_dataset.py -f sampledata/Study300002_HMSL10008_sorafenib_ambit.xls | ||
| check_errs $? "import study dataset fails" | ||
|
|
||
| python src/import_libraries.py -f sampledata/libraries.xls | ||
| check_errs $? "import library fails" | ||
|
|
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| python src/create_indexes.py | psql -U devlincsweb devlincs -h dev.pgsql.orchestra -v ON_ERROR_STOP=1 | ||
| #check_errs $? "create indexes fails" |