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#1498757028
cd pipeline_template_data/
#1498757028
ll
#1498757031
cat Dummy.rst 
#1498757036
rm -f Dummy.rst 
#1498757040
cat Methods.rst 
#1498757043
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cat TemplateReport.py 
#1498757050
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ll
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#1498757075
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ll
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ll
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vim sphinxreport.ini 
#1498757122
ll themes/
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ll themes/cgat/
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vimdiff pipeline_template_full.py pipeline_template_minimal.py 
#1498757193
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ll
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#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
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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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cd templates/
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ll
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vim pipeline_template.ini 
#1498843698
vim pipeline_template.py 
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vim sphinxreport.ini 
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l
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ls -R
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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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cd -
#1499105096
ll
#1499105166
mv rsync_cmd.rst rsync_cmd.txt
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cd AntonioJBT/project_quickstart/templates/
#1499105766
ll
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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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ll
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cd templates/
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ll
#1499171872
ll version.py 
#1499171877
vim version.py 
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ls -alA
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#1499179043
ll
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mv rsync_cmd.txt rsync_cmd_template.txt
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cd templates/
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ll
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cd templates/
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ll
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cd docs
#1499190885
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#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 .
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cd templates/
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ll
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#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 
#1504357063
cd templates/
#1504357063
ll
#1504357075
find . -iname "Makefile"
#1504357090
find . -iname "Makefile" | ll
#1504357100
find . -iname "Makefile" < ll
#1504357111
find . -iname "Makefile" | ll -
#1504357118
ll < find . -iname "Makefile"
#1504357124
find . -iname "Makefile"
#1504357129
ll ./project_template/docs/Makefile
#1504357140
ll report_templates/Makefile
#1504357146
ll script_templates/pipeline_template/configuration_pipeline_template/Makefile
#1504357154
vim project_template/docs/Makefile 
#1504357296
vim project_template/docs/conf.py 
#1504357592
vim project_template/docs/Makefile 
#1504357601
vim project_template/docs/conf.py 
#1504357639
vim script_templates/pipeline_template/configuration_pipeline_template/pipeline_template.ini 
#1504357654
vim project_template/docs/conf.py 
#1504358162
vim script_templates/pipeline_template/configuration_pipeline_template/pipeline_template.ini 
#1504358326
vim -O2 script_templates/pipeline_template/configuration_pipeline_template/pipeline_template.ini ../project_quickstart.ini 
#1504358619
vim script_templates/pipeline_template/configuration_pipeline_template/pipeline_template.ini
#1504360336
vim script_templates/pipeline_template/pipeline_template.py 
#1504361958
vim script_templates/pipeline_template/pipeline_template.py 
#1504362307
pwd
#1504362324
vim script_templates/pipeline_template/pipeline_template.py 
#1504598048
source activate py35t
#1504898643
..
#1505151614
..
#1505220740
..
#1505245032
..
#1505325994
..
#1505404066
..
#1505412746
..
#1505412915
cd templates/
#1505412916
ll
#1505412919
ll script_templates/
#1505412922
ll report_templates/
#1505412940
ll
#1505465969
cd templates/
#1505465970
ll
#1505474375
..
#1505497364
..
#1505747894
..
#1505844793
..
#1505845661
..
#1505914758
..
#1505914770
cd -
#1505918133
..
#1505918140
vim script_templates/pipeline_template/pipeline_template.py 
#1505920386
ll examples/
#1505920387
ll
#1505920389
ll examples/
#1505920543
ls -1
#1505920549
ls -1 examples/
#1505923265
ll
#1505923360
imperial 
#1505923735
vim script_templates/pipeline_template/pipeline_template.py 
#1505924014
ll
#1505931353
ll script_templates/
#1505932573
..
#1505933342
..
#1506943417
..
#1506955712
..
#1507110478
cd ..
#1507218853
..
#1507661578
..
#1507730654
..
#1507737277
..
#1507737361
cd AntonioJBT/project_quickstart/templates/
#1507737362
ll
#1507737388
..
#1507739309
cd AntonioJBT/project_quickstart/templates/
#1507739310
ll
#1507739313
ll report_templates/
#1507739319
ll project_template/
#1507739320
ll
#1507739325
ll script_templates/
#1507739398
cp examples/ggtheme.R .
#1507739526
cp examples/pipeline_pq_example/configuration_pipeline_pq_example/scipy_references.bib script_templates/pipeline_template/configuration_pipeline_template/
#1507739541
cp examples/pipeline_pq_example/configuration_pipeline_pq_example/report_substitution_vars.rst script_templates/pipeline_template/configuration_pipeline_template/
#1508174389
cd AntonioJBT/project_quickstart/templates/
#1508174402
ll report_templates/
#1509650573
cd AntonioJBT/project_quickstart/templates/
#1509650573
ll
#1509650625
..
#1510061164
cd AntonioJBT/project_quickstart/templates/
#1510061165
ll
#1510061177
open script_templates/template.R
#1510061515
head script_templates/template.py 
#1510061518
vim script_templates/template.py 
#1510593000
..
#1510593001
ll
#1511191060
..
#1511191061
ll
#1511191078
ll project_template/docs/
#1511191091
ll script_templates/pipeline_template/configuration_pipeline_template/
#1511191105
ll
#1511191114
ll report_templates/
#1511191149
vimdiff report_templates/manuscript_template.rst script_templates/pipeline_template/configuration_pipeline_template/report_pipeline_template.rst 
#1511191188
vim script_templates/pipeline_template/configuration_pipeline_template/report_pipeline_template.rst 
#1511191221
vim script_templates/pipeline_template/configuration_pipeline_template/report_substitution_vars.rst 
#1511191252
cp examples/pipeline_pq_example/configuration_pipeline_pq_example/report_pipeline_pq_example.rst script_templates/pipeline_template/configuration_pipeline_template/
#1513274757
cd AntonioJBT/project_quickstart/templates/
#1513274758
ll
#1513275111
..
#1513340841
cd AntonioJBT/project_quickstart/templates/
#1513340842
ll
#1513340857
..
#1513341020
cd templates/
#1513341023
ll
#1513341033
mv ggtheme* script_templates/
#1513341034
ll
#1515427644
..
#1515429680
..
#1516205795
cd templates/
#1516205796
ll
#1516205810
touch script_templates/__init__.py
#1516205825
touch project_template/tests/__init__.py
#1516205856
ll
#1516205859
ll script_templates/
#1516205867
ll examples/
#1516205881
touch examples/__init__.py
#1516205898
touch examples/pipeline_pq_example/__init__.py
#1528198340
..
#1528198345
vim README_data.rst 
#1528198350
ll
#1528199203
..
#1528199204
ll
#1528199212
cat TO_DO.rst 
#1528218460
cd templates/
#1528218461
ll
#1528218465
cat TO_DO.rst 
#1528222251
..
#1528813016
cd templates/
#1528813017
ll
#1528813030
..
#1528813030
ll
#1528813036
ll project_template/
#1528813040
ll project_template/project_template
#1528820722
..
#1528820723
ll
#1528820737
ll project_template/
#1528820741
ll project_template/project_template
#1528820756
vim project_template/Dockerfile 
#1528821233
..
#1528822819
..
#1528825011
..
#1529515072
cd templates/
#1529515073
ll
#1529515089
grep -rne "P.run" .
#1529515106
vim ./script_templates/pipeline_template/pipeline_template.py
#1529515129
grep -rne "P.run" .
#1529515440
ll
#1529516117
cd templates/
#1529516118
ll
#1529516126
ll examples/
#1529517407
cat find_cmd.sh 
#1529517412
type find_cmd.sh 
#1529517451
cat < $type find_cmd.sh
#1529517458
ll
#1529517482
cat < ${type find_cmd.sh}
#1529517482
cat < ${type find_cmd.sh}
#1529517488
cat < echo ${type find_cmd.sh}
#1529517499
echo ${type find_cmd.sh}
#1529517508
{type find_cmd.sh}
#1529517520
cat  /Users/antoniob/Documents/github.dir/AntonioJBT/various.dir/scripts/find_cmd.sh
#1529517542
vim /Users/antoniob/Documents/github.dir/AntonioJBT/various.dir/scripts/find_cmd.sh
#1529517568
find_cmd.sh "*ini"
#1529517579
find_cmd.sh "*ini" .
#1529517586
vim /Users/antoniob/Documents/github.dir/AntonioJBT/various.dir/scripts/find_cmd.sh
#1529517626
find_cmd.sh . "*ini"
#1529517644
find_cmd.sh . "*.ini"
#1529517660
find_cmd.sh . "*.ini" | grep ini
#1529519011
..
#1529609717
cd templates/
#1529609718
ll
#1529668262
cd templates/
#1529668263
ll
#1529668271
ll examples/
#1529669144
ll
