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antoniob has entered /Users/antoniob/Documents/github.dir/AntonioJBT/tests_and_bugs/pipe_quick_test/pipeline_template_data from /Users/antoniob/Documents/github.dir/AntonioJBT/tests_and_bugs/pipe_quick_test
#1498757028
cd pipeline_template_data/
#1498757028
ll
#1498757031
cat Dummy.rst 
#1498757036
rm -f Dummy.rst 
#1498757040
cat Methods.rst 
#1498757043
rm -f Methods.rst 
#1498757047
cat TemplateReport.py 
#1498757050
rm -f TemplateReport.py 
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ll
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cat __init__.py 
#1498757058
rm -f __init__.py 
#1498757064
rm -f cgat_logo.png 
#1498757070
cat conf.py 
#1498757075
vim conf.py 
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ll
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rm -f conf.py 
#1498757096
cat contents.rst 
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ll
#1498757109
rm -f contents.rst pipeline.rst 
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vim sphinxreport.ini 
#1498757122
ll themes/
#1498757124
ll themes/cgat/
#1498757127
rm -rf themes/
#1498757128
ll
#1498757140
vimdiff pipeline_template_full.py pipeline_template_minimal.py 
#1498757193
rm -f pipeline_template_minimal.py 
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ll
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antoniob has exited /Users/antoniob/Documents/github.dir/AntonioJBT/tests_and_bugs/pipe_quick_test/pipeline_template_data for ..
#1498843030
mv pipeline_template_data_bones/* .
#1498843033
la pipeline
#1498843038
la pipeline_template_data_bones/
#1498843044
rm -rf pipeline_template_data_bones
#1498843046
ll
#1498843060
mv pipeline.ini pipeline_template.ini
#1498843090
mv pipeline_template_full.py pipeline_template.py
#1498843094
ll
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ll project_template/
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ll project_template/project_template
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ll
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antoniob has exited /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates for ..
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antoniob has entered /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates from /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart
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cd templates/
#1498843544
ll
#1498843549
vim pipeline_template.ini 
#1498843698
vim pipeline_template.py 
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vim sphinxreport.ini 
#1498845343
rm -f sphinxreport.ini 
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ll
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antoniob has exited /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates for ..
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antoniob has entered /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates from /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart
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cd templates/
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l
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ll
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ll project_template/
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antoniob has entered /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates from /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates/project_template
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..
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ls -R
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ll
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antoniob has exited /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates for ..
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antoniob has entered /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates from /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart
#1499104647
cd templates/
#1499104648
ls
#1499104661
vim rsync_cmd.sh
#1499104978
mv rsync_cmd.sh rsync_cmd.rst
#1499105011
vim rsync_cmd.rst 
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ll
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antoniob has entered /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates from /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart
#1499105095
cd -
#1499105096
ll
#1499105166
mv rsync_cmd.rst rsync_cmd.txt
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antoniob has entered /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates from /Users/antoniob/Documents/github.dir
#1499105765
cd AntonioJBT/project_quickstart/templates/
#1499105766
ll
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antoniob has exited /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates for -
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antoniob has entered /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates from /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart
#1499108031
cd templates/
#1499108033
vim rsync_cmd.txt 
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antoniob has exited /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates for ..
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antoniob has entered /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates from /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart
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cd templates/
#1499108559
ll
#1499108631
vim substitution_vars.rst 
#1499108709
vim -O2 template.py pipeline_template.py 
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antoniob has exited /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates for ..
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antoniob has entered /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates from /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart
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cd templates/
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ll
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antoniob has exited /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates for project_template/
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antoniob has entered /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates from /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates/project_template
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..
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antoniob has exited /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates for ..
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antoniob has entered /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates from /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart
#1499171867
cd templates/
#1499171868
ll
#1499171872
ll version.py 
#1499171877
vim version.py 
#1499171891
antoniob has exited /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates for project_template/
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antoniob has entered /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates from /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates/project_template
#1499172397
..
#1499172400
ls -alA
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antoniob has exited /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates for ..
#1499179042
antoniob has entered /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates from /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart
#1499179042
cd templates/
#1499179043
ll
#1499179055
mv rsync_cmd.txt rsync_cmd_template.txt
#1499180177
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antoniob has entered /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates from /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart
#1499189232
cd templates/
#1499189233
ll
#1499189238
antoniob has exited /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates for project_template/
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antoniob has entered /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates from /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates/project_template
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..
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antoniob has exited /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates for ..
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antoniob has entered /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates from /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart
#1499190877
cd templates/
#1499190878
ll
#1499190881
antoniob has exited /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates for docs
#1499190881
antoniob has entered /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates from /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart
#1499190881
cd docs
#1499190885
antoniob has exited /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates for project_template/
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antoniob has entered /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates from /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates/project_template
#1499192352
..
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antoniob has exited /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates for ..
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antoniob has entered /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates from /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart
#1499265890
cd templates/
#1499265896
grep -rn Antonio .
#1499265943
grep -rn Antonio --exclude dir_bash .
#1499265962
grep -rn Antonio --exclude=dir_bash .
#1499265978
grep -rn Antonio --exclude=*dir_bash .
#1499265988
grep -rn Antonio --exclude=*dir_bash* .
#1499266008
grep -rn Berlanga .
#1499266013
antoniob has exited /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates for ..
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antoniob has entered /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates from /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart
#1500297401
cd templates/
#1500297402
ll
#1500302409
antoniob has exited /Users/antoniob/Documents/github.dir/AntonioJBT/project_quickstart/templates for ..
#1500915368
cd Documents/github.dir/AntonioJBT/project_quickstart/templates/
#1500915370
lla
#1500915391
vim README_data.txt
#1501691401
cd templates/
#1501691401
lla
#1501691403
ll
#1501692078
cd templates/
#1501692079
ll
#1501692105
cp ../templates/project_template/docs/conf.py .
#1501692121
cp ../templates/project_template/docs/Makefile .
#1501692137
cp ../templates/project_template/docs/make.bat .
#1501692149
cp ../templates/project_template/docs/*rst .
#1501692151
ll
#1501692155
rm -rf scripts.rst 
#1501692166
rm -f modules.rst 
#1501692167
ll
#1501692203
mkdir report_configs
#1501692204
ll
#1501692222
mv include_links.rst index.rst make.bat Makefile conf.py report_configs/
#1501692223
ll
#1501692262
mkdir report_templates
#1501692286
mv manuscript_template.rst DAP_template.rst lab_notebook_template.rst cover_letter_template.rst report_templates/
#1501692289
ll
#1501692299
mkdir script_templates
#1501692306
mv template.* script_templates/
#1501692307
ll
#1501692322
mv pipeline_template.* script_templates/
#1501692323
ll
#1501692331
mv module_template.py script_templates/
#1501692333
ll
#1501692336
cat version.py 
#1501692340
mv version.py script_templates/
#1501692341
ll
#1501692356
cat substitution_vars.rst 
#1501692447
mv substitution_vars.rst file_with_include.rst report_templates/
#1501692448
ll
#1501692529
cat report_templates/substitution_vars.rst 
#1501692550
cat project_template/project_template.ini 
#1501692645
cat report_templates/file_with_include.rst 
#1501693430
..
#1501693431
ll
#1501693554
..
#1501693555
ll
#1501693561
cat README_data.txt 
#1501693566
ll
#1501694431
..
#1501694507
cd templates/
#1501694508
ll
#1501694784
ll report_*
#1501694878
mv report_configs/* report_templates/
#1501694883
lla report_configs/
#1501694889
rm -rf report_configs
#1501694890
ll
#1501696788
..
#1501696839
cd templates/
#1501696841
ll
#1501696853
cat TO_DO_template.txt 
#1501696869
vim TO_DO_template.txt 
#1501696914
ll
#1501696928
mv TO_DO_template.txt TO_DO_template.rst
#1501696930
ll
#1501696941
mv README_data.txt README_data.rst
#1501696950
mv rsync_cmd_template.txt rsync_cmd_template.rst
#1501696957
ll
#1501697163
ll report_templates/
#1501697928
ll
#1501697930
ll script_templates/
#1501786310
cd templates/
#1501786311
lla
#1501786313
ll
#1501786342
mv TO_DO_template.rst TO_DO.rst 
#1501786389
mv rsync_cmd_template.rst to rsync,rst
#1501786396
mv rsync_cmd_template.rst rsync.rst
#1501786397
lla
#1501786413
ll -R
#1501786454
pip -h
#1501786466
pip uninstall project_quickstart
#1501837294
cd AntonioJBT/project_quickstart/templates/
#1501837295
lla
#1501837296
ll
#1501865116
..
#1501865187
..
#1501865661
..
#1501866408
..
#1501868681
..
#1502373731
..
#1502373734
ll
#1502374521
..
#1502374522
ll
#1502454675
..
#1502454676
ll
#1502454681
ll report_templates/
#1502454686
ll script_templates/
#1502455536
..
#1502457159
cd -
#1502457161
ll
#1502457163
ll script_templates/
#1502457172
ll script_templates/pipeline_template/
#1502457374
..
#1502457374
ll
#1502457451
..
#1502458042
ll
#1502458305
..
#1502458306
ll
#1502458329
ll report_templates/
#1502458375
ll script_templates/
#1502458391
ll script_templates/pipeline_template/
#1502472247
cd templates/
#1502472248
ls
#1502472262
ls -lR project_template/
#1502472273
ls -lR report_templates/
#1502472301
vim ../.gitignore 
#1502472344
pwd
#1502472367
..
#1502472369
vim ../.gitignore 
#1502472415
ll
#1502472419
ll script_templates/
#1502472422
ll script_templates/pipeline_template/
#1502739562
cd templates/
#1502739563
ll
#1502739567
ll script_templates/
#1502739571
ll script_templates/pipeline_template/
#1502740664
ll
#1502740667
ll script_templates/pipeline_template/
#1502740698
xs script_templates/pipeline_template/
#1502740701
cs script_templates/pipeline_template/
#1502740702
ll
#1504266831
cd AntonioJBT/project_quickstart/templates/
#1504266831
lla
#1504266837
ll report_templates/
#1504266890
ll script_templates/
#1504266895
ll script_templates/pipeline_template/
#1504266928
ll script_templates/pipeline_template/configuration_pipeline_template/
#1504274931
lla
#1504274936
ll project_template/
#1504274940
ll project_template/docs/
#1504274948
ll
#1504274950
ll script_templates/
#1504274956
ll script_templates/pipeline_template/
#1504274958
ll script_templates/pipeline_template/configuration_pipeline_template/
#1504274968
ll report_templates/
#1504274973
ll
#1504276256
cd templates/
#1504276265
find . -iname "*TO*"
#1504276277
find . -iname "*TO_DO*"
#1504277510
cd templates/
#1504277515
ll 
