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git-stuff
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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
#
cd /home/suvinit/NEAT && git branch && git checkout master && git pull
#
cd /home/suvinit/NEAT && git checkout blast && git add /home/suvinit/NEAT/blast/ && git status && git push origin blast && git fetch
#
git config --global --unset credential.helper
git config credential.helper store
git config user.email "[email protected]"
git config --local user.email "[email protected]"
git init
git clone https://github.com/VarenyaJ/repo.git
git clone https://github.com/ncsa/NEAT.git
#
old config stuffs:{
cp /home/suvinit/blast /home/suvinit/upload-to-NCSA-NEAT/
85 cp -rf /home/suvinit/blast /home/suvinit/upload-to-NCSA-NEAT/
86 cd upload-to-NCSA-NEAT/
87 git config user.email "[email protected]"
88 git config
89 git config --local user.email "[email protected]"
90 clear
91 git init
92 git add -a
93 git add -A
94 cd ..
95 rm -rfi upload-to-NCSA-NEAT/
96 cd upload-to-NCSA-NEAT/
97 rm -rfi
98 rm --help
99 rm -rf -r
100 rm -rf -i
101 cd ..
102 rm -rf upload-to-NCSA-NEAT/
103 clear
104 cp /home/suvinit/blast /home/suvinit/neat-upload
105 cp -rf /home/suvinit/blast /home/suvinit/neat-upload
106 clear
107 cd neat-upload/
108 git init
109 ls -la
110 rm -rf .git
111 ls -la
112 git init /home/suvinit/neat-upload/
113 git config user.name "VarenyaJ"
114 git config user.email "[email protected]"
115 git clone https://github.com/ncas/NEAT.git
116 https://github.com/VarenyaJ/repo.git
117 git clone https://github.com/VarenyaJ/repo.git
118 git clone https://github.com/ncsa/NEAT.git
119 git checkout
120 git checkout -b
121 git branch -a
122 git branch
123 git checkout
124 branch
125 git branch --help
126 git branch --list
127 git checkout -b blast
128 git status
129 ls
130 rm -rf NEAT
131 git config
132 clear
133 git commit -m "create blast branch and push some local files"
134 git add -A
135 git commit -m "create blast branch and push some local files"
136 git push origin blast
137 git clone https://github.com/ncsa/NEAT.git
138 ls
139 cd NEAT/
140 ls
141 rm -rf
142 ls
143 clear
144 ls
145 rm bacterial_genreads_wrapper.py
146 rm gen_reads
147 rm gen_reads_parallel.py
148 rm requirements.txt
149 rm ChangeLog.md
150 rm LICENSE.md
151 rm setup.py
152 rm CODE_OF_CONDUCT.md
153 rm CONTRIBUTING.md
154 rm docs/
155 clear
156 ls
157 rm docs rm gen_reads.py
158 clear && ls
159 rm README.md
160 rm source/
161 rm -rf source/
162 rm -rf utilities/
163 rm -rf docs/
164 rm -rf models/
165 ls
166 clear
167 ls -la
168 rm -rf
169 ls -la
170 rm -rf .git
171 rm -rf .github/
172 rm -rf .idea/
173 rm .gitignore
174 rm .gitattributes
175 ls
176 clear
177 ls -la
178 rm -rf ..
179 rm -rf ".."
180 clear
181 ls -la
182 cd ..
183 ls
184 mkdir blast
185 cp db blast/
186 cp -r db blast/
187 rm -rf blast/
188 clear
189 ls
190 mv /db /blast
191 mv db/ blast/
192 ls
193 mv ncbi-blast-2.12.0+/ blast/
194 clear
195 ls
196 mv H1N1-vs-swissprot.out/ blast/
197 mv H1N1-vs-swissprot.out blast/
198 clear && ls
199 mv blast/ NEAT/
200 clear
201 git checkout
202 git branch
203 git branch -a
204 clear
205 git remote add origin https://github.com/ncsa/NEAT
206 git branch -a
207 git add -A
208 git commit -m "create blast branch andd add some files"
209 git push origin blast
210 git pull
211 git branch -a
212 git checkout /origin/blast
213 git checkout remotes/origin/blast
214 git switch
215 git revert
216 exit
217 history
}
#
05.24.2022
<>:{
1 history -w
2 clear
3 exit
4 history
5 cd && sudo apt install git libasound2 libcurl4 libgbm1 libgcrypt20 libgtk-3-0 libnotify4 libnss3 libglib2.0-bin xdg-utils libx11-xcb1 libxcb-dri3-0 libxss1 libxtst6 libxkbfile1 && cd /home/suvinit/Downloads && tar xf atom-amd64.tar.gz && atom
6 atom
7 cd
8 cat /home/suvinit/Desktop/update-thingies.sh
9 cd && sudo apt-get update -y && sudo apt-get upgrade -y && uname -sr && python3 --version && neofetch
10 touch test_click.py
11 python3 test_click.py
12 touch test_command.py
13 python3 test_command.py
14 python3 cli-test.py
15 python3 cli-test.py hello
16 history
17 clear
18 cd && sudo apt-get update -y && sudo apt-get upgrade -y && uname -sr && python3 --version && neofetch && sudo apt install snapd && sudo snap install atom --classic
19 cd
20 cd NEAT
21 git branch
22 mv /home/suvinit/Desktop/cli-test.py /home/suvinit/NEAT
23 mv /home/suvinit/Desktop/test_click.py /home/suvinit/NEAT
24 mv /home/suvinit/Desktop/test_command.py /home/suvinit/NEAT
25 git add cli-test.py
26 git add test_click.py
27 git add test_command.py
28 git push
29 cd && sudo apt-get update -y && sudo apt-get upgrade -y && uname -sr && python3 --version && neofetch
30 git branch
31 git branch master
32 git checkout master
33 git pull
34 git checkout command_script
35 git pull
36 python3 test_click.py
37 python3 cli-test.py
38 python3 test_command.py
39 pwd
40 /home/suvinit/blast
41 python3 Desktop/parts-command_script.py
42 pwd
43 python3 /home/suvinit/Desktop/parts-command_script.py
44 python3 /home/suvinit/Desktop/cli-test.py
45 python3 /home/suvinit/Desktop/test_command.py
46 cd /home/suvinit/Desktop/ && ./update-thingies.sh && cd
47 clear
48 cd /home/suvinit/NEAT
49 clear
50 cd /home/suvinit/NEAT-data/
51 ls
52 ls H1N1/
53 pwd
54 cd ..
55 pwd
56 cd .. && pwd
57 ls
58 cd && sudo apt-get update -y && sudo apt-get upgrade -y && uname -sr && python3 --version && neofetch
59 cd NEAT
60 python3 constant-click-test.py
61 pwd
62 ls ..
63 python3 constant-click-test.py
64 clear
65 python3 constant-click-test.py
66 python3 2constant-click-test.py
67 python3
68 clear
69 pwd
70 clear
71 pwd && ls
72 python3 test_click.py
73 python3 test_command.py
74 python3 constant-click-test.py
75 python3 test_click.py
76 python3 constant-click-test.py
77 python3 cli-test.py
78 cd && xrandr --output Virtual1 --mode 1920x1080
79 cd /home/suvinit/Desktop/ && ./updatethingies.sh && cd /home/suvinit/NEAT && clear && pwd && ls
80 cd /home/suvinit/Desktop/ && ./update-thingies.sh && cd /home/suvinit/NEAT && clear && pwd && ls
81 python3 test_command.py
82 python3 test_click.py
83 python3 test_command.py
84 python3 test_command.py --file_path h1n1.fake.bed
85 python3 test_command.py --file_path /home/suvinit/NEAT-data/H1N1/h1n1.fake.bed
86 python3 test_command.py --file_path /home/suvinit/NEAT-data/H1N2
87 python3 test_command.py --output_path /home/suvinit/NEAT-data/H1N2
88 git branch
89 git add test_command.py
90 git commit -m "foundation for using three flags"
91 git config user.name "VarenyaJ"
92 git config user.email "[email protected]"
93 git add test_command.py
94 git commit -m "foundation for using three flags"
95 git checkout
96 git status
97 git push
98 git config user.email "[email protected]"
99 clear
100 cd && sudo apt-get update -y && sudo apt-get upgrade -y && uname -sr && python3 --version && neofetch
101 cd /home/suvinit/NEAT/testing_command_script/
102 python3 test_command.py
103 python3 random-trial-click-test.py
104 python3 random-trial-click-test.py --help
105 python3 random-trial-click-test.py --gr True
106 python3 random-trial-click-test.py --gr TRUE
107 python3 random-trial-click-test.py --help
108 clear
109 python3 random-trial-click-test.py --help
110 python3 random-trial-click-test.py --n 14
111 python3 random-trial-click-test.py --n 14 --gr
112 python3 random-trial-click-test.py --n 14 --br
113 python3 random-trial-click-test.py --n 14 --gr
114 python3 random-trial-click-test.py --n 14
115 python3 random-trial-click-test.py
116 python3 random-trial-click-test.py --n 14
117 python3 random-trial-click-test.py
118 python3 test_command.py
119 python3 random-trial-click-test.py
120 python3 2test_command.py
121 python3 test_command.py
122 python3 2test_command.py
123 python3 random-trial-click-test.py
124 python3 random-trial-click-test.py -help
125 python3 random-trial-click-test.py --help
126 python3 random-trial-click-test.py --gr
127 python3 random-trial-click-test.py --br
128 python3 random-trial-click-test.py --gr TRUE
129 python3 random-trial-click-test.py --br FALSE
130 python3 random-trial-click-test.py --n 14
131 python3 random-trial-click-test.py -gr
132 python3 random-trial-click-test.py --gr
133 python3 random-trial-click-test.py --br
134 python3 random-trial-click-test.py --br --n 14
135 python3 random-trial-click-test.py --gr --n 14
136 python3 2test_command.py
137 python3 2test_command.py --help
138 python3 2test_command.py --bam
139 python3 test_command.py
140 python3 test_command.py --br
141 python3 test_command.py --gr
142 python3 test_command.py --gr --n 14
143 python3 test_command.py --gr --bam
144 python3 test_command.py
145 python3 test_command.py --bam
146 history
}
#
06???
git branch -a
git checkout <>
git config user.email "[email protected]"
git config user.name "VarenyaJ"
git add
git commit -m ""
git status
git push
################
06.13.2022
#git pull origin feature/parallelization
#git push --set-upstream origin command_script
#ssh-keygen -t ed25519 -C "[email protected]"
#cat ~/.ssh/id_ed25519.pub
<>:{
history -w
2 clear
3 exit
4 history
5 cd && sudo apt install git libasound2 libcurl4 libgbm1 libgcrypt20 libgtk-3-0 libnotify4 libnss3 libglib2.0-bin xdg-utils libx11-xcb1 libxcb-dri3-0 libxss1 libxtst6 libxkbfile1 && cd /home/suvinit/Downloads && tar xf atom-amd64.tar.gz && atom
6 atom
7 cd
8 cat /home/suvinit/Desktop/update-thingies.sh
9 cd && sudo apt-get update -y && sudo apt-get upgrade -y && uname -sr && python3 --version && neofetch
10 touch test_click.py
11 python3 test_click.py
12 touch test_command.py
13 python3 test_command.py
14 python3 cli-test.py
15 python3 cli-test.py hello
16 history
17 clear
18 cd && sudo apt-get update -y && sudo apt-get upgrade -y && uname -sr && python3 --version && neofetch && sudo apt install snapd && sudo snap install atom --classic
19 cd
20 cd NEAT
21 git branch
22 mv /home/suvinit/Desktop/cli-test.py /home/suvinit/NEAT
23 mv /home/suvinit/Desktop/test_click.py /home/suvinit/NEAT
24 mv /home/suvinit/Desktop/test_command.py /home/suvinit/NEAT
25 git add cli-test.py
26 git add test_click.py
27 git add test_command.py
28 git push
29 cd && sudo apt-get update -y && sudo apt-get upgrade -y && uname -sr && python3 --version && neofetch
30 git branch
31 git branch master
32 git checkout master
33 git pull
34 git checkout command_script
35 git pull
36 python3 test_click.py
37 python3 cli-test.py
38 python3 test_command.py
39 pwd
40 /home/suvinit/blast
41 python3 Desktop/parts-command_script.py
42 pwd
43 python3 /home/suvinit/Desktop/parts-command_script.py
44 python3 /home/suvinit/Desktop/cli-test.py
45 python3 /home/suvinit/Desktop/test_command.py
46 cd /home/suvinit/Desktop/ && ./update-thingies.sh && cd
47 clear
48 cd /home/suvinit/NEAT
49 clear
50 cd /home/suvinit/NEAT-data/
51 ls
52 ls H1N1/
53 pwd
54 cd ..
55 pwd
56 cd .. && pwd
57 ls
58 cd && sudo apt-get update -y && sudo apt-get upgrade -y && uname -sr && python3 --version && neofetch
59 cd NEAT
60 python3 constant-click-test.py
61 pwd
62 ls ..
63 python3 constant-click-test.py
64 clear
65 python3 constant-click-test.py
66 python3 2constant-click-test.py
67 python3
68 clear
69 pwd
70 clear
71 pwd && ls
72 python3 test_click.py
73 python3 test_command.py
74 python3 constant-click-test.py
75 python3 test_click.py
76 python3 constant-click-test.py
77 python3 cli-test.py
78 cd && xrandr --output Virtual1 --mode 1920x1080
79 cd /home/suvinit/Desktop/ && ./updatethingies.sh && cd /home/suvinit/NEAT && clear && pwd && ls
80 cd /home/suvinit/Desktop/ && ./update-thingies.sh && cd /home/suvinit/NEAT && clear && pwd && ls
81 python3 test_command.py
82 python3 test_click.py
83 python3 test_command.py
84 python3 test_command.py --file_path h1n1.fake.bed
85 python3 test_command.py --file_path /home/suvinit/NEAT-data/H1N1/h1n1.fake.bed
86 python3 test_command.py --file_path /home/suvinit/NEAT-data/H1N2
87 python3 test_command.py --output_path /home/suvinit/NEAT-data/H1N2
88 git branch
89 git add test_command.py
90 git commit -m "foundation for using three flags"
91 git config user.name "VarenyaJ"
92 git config user.email "[email protected]"
93 git add test_command.py
94 git commit -m "foundation for using three flags"
95 git checkout
96 git status
97 git push
98 git config user.email "[email protected]"
99 clear
100 cd && sudo apt-get update -y && sudo apt-get upgrade -y && uname -sr && python3 --version && neofetch
101 atom
102 cd /home/suvinit/Desktop/ && cat updatethingies.sh
103 cd /home/suvinit/Desktop
104 ls
105 cat commas.txt
106 cat update-thingies.sh
107 ./update-thingies.sh
108 pwd
109 touch some-command-line-history
110 cat /home/suvinit/Desktop/update-thingies.sh
111 cd /home/suvinit/Desktop
112 ./update-thingies.sh
113 cd /home/suvinit/Desktop/
114 ./update-thingies.sh
115 cd /home/suvinit/Desktop/ && ./updatethingies.sh
116 cd /home/suvinit/Desktop/ && ./update-thingies.sh
117 python3 readingALPHA.py
118 clear && python3 readingALPHA.py
119 lear && python3 readingALPHA.py
120 clear && python3 readingALPHA.py
121 cd /home/suvinit/Desktop/
122 ./update-thingies.sh
123 cd
124 cd /home/suvinit/NEAT/testing_command_script/
125 python3 test_command.py --file_path /home/suvinit/NEAT-data/H1N1/H1N1.fa --read_length 250 --output_path /home/suvinit/Desktop/
126 clear && python3 test_command.py --file_path /home/suvinit/NEAT-data/H1N1/H1N1.fa --read_length 250 --output_path /home/suvinit/Desktop/
127 cd /home/suvinit/Desktop/
128 ./update-thingies.sh
129 clear && python3 readingALPHA.py
130 clear && python3 readingBETA.py
131 clear && python3 readingALPHA.py
132 git pull origin feature/parallelization
133 clear && python3 readingALPHA.py
134 cd /home/suvinit/Desktop/
135 ./update-thingies.sh
136 cd /home/suvinit/Desktop/
137 ./update-thingies.sh
138 cd ../NEAT/testing_command_script/
139 clear
140 ls
141 git status
142 git add reading.py readingALPHA.py readingBETA.py config.txt neat.cfg test_command.py
143 git commit -m "pushing current files"
144 git branch
145 clear
146 git status
147 git add reading.py readingALPHA.py readingBETA.py config.txt neat.cfg test_command.py
148 git commit -m "pushing current files"
149 cd ..
150 cd ../../Desktop/
151 ls
152 cat commas.txt
153 cat git-stuff
154 cd ..
155 ls
156 ls command_script/
157 cd command_script/
158 cd /home/suvinit/Desktop/
159 touch Token-06.13.2022
160 vim Token-06.13.2022
161 cd ..
162 git pull origin feature/parallelization
163 pwd
164 git pull origin feature/parallelization
165 git pull
166 git branch
167 ls
168 git branch master
169 git checkout master
170 cd ..
171 ls
172 rm -rf NEAT
173 ls
174 git pull https://github.com/ncsa/NEAT.git
175 git clone https://github.com/ncsa/NEAT.git
176 ls
177 clear && ls
178 cd NEAT
179 git branch
180 git branch --list
181 git checkout
182 git branch --a
183 git branch -a
184 clear
185 git branch -a
186 git checkout command_script
187 git pull origin feature/parallelization
188 git config --global user.email [email protected]
189 git config --global user.name VarenyaJ
190 git pull origin feature/parallelization
191 cleatr
192 clear
193 cd ..
194 ls
195 cd NEAT
196 ls
197 ls -lar
198 clear
199 git branch -a
200 git checkout blast
201 bit branch
202 git branch
203 clear
204 git branch -a
205 git checkout remotes/origin/blast
206 clear
207 cd
208 cd Desktop/
209 mv /home/suvinit/Desktop/command_script/ /home/suvinit/
210 cd ..
211 ls
212 clear
213 ls
214 rm -rf NEAT
215 clear
216 cd Desktop/
217 ./update-thingies.sh
218 cd ..
219 clear && l
220 clear && ls
221 git clone https://github.com/ncsa/NEAT.git
222 ls
223 cd NEAT
224 git branch -a
225 git checkout command_script
226 ls
227 git pull origin feature/parallelization
228 cd ..
229 rm -rf NEAT
230 git clone https://github.com/ncsa/NEAT.git
231 cd NEAT
232 git checkout feature/parallelization
233 git branch command_script
234 ls
235 git branch -a
236 git checkout command_script
237 clear
238 ls
239 clear
240 ls
241 git add command_script/
242 git commit -m "re-make command_script repo"
243 git status
244 git push
245 git push --set-upstream origin command_script
246 ls -al ~/.ssh
247 ssh-keygen -t ed25519 -C "[email protected]"
248 eval "$(ssh-agent -s)"
249 ssh-add ~/.ssh/id_ed25519
250 cat ~/.ssh/id_ed25519.pub
251 git push --set-upstream origin command_script
252 git clone https://github.com/VarenyaJ/repo.git
253 cat /home/suvinit/Desktop/Token-06.13.2022
254 git clone https://github.com/VarenyaJ/repo.git
255 git config
256 git
257 clear
258 clear && python3 test_command.py
259 clear && python3 kappa.py
260 cd ..
261 cd NEAT
262 git branch -a
263 git pull origin feature/parallelization
264 touch testpush.txt
265 git add testpush.txt
266 git push
267 git push --set-upstream origin command_script
268 ls .git
269 cd .git
270 cd .config
271 cat config
272 vim config
273 cd ..
274 ls
275 git add testpush.txt
276 git push
277 git add testpush.txt
278 git commit
279 git commit -m "testing push"
280 git push --set-upstream origin command_script
281 ls
282 cp /home/suvinit/command_script/ /home/suvinit/NEAT
283 clear
284 ls
285 cp -r /home/suvinit/command_script/ /home/suvinit/NEAT
286 clear && ls
287 ls command_script/
288 git add command_script/
289 git commit -m "adding back files"
290 git push
291 clear
292 history
}
################
06.28.2022-07.01.2022
<>:{
cd /home/suvinit
rm -rf NEAT
git clone [email protected]:ncsa/NEAT.git
cd NEAT
git checkout feature/modularization
git checkout -b modular/command_script
ls
history
git status
git add *
git commit m "added some command_script files"
git commit -m "added some command_script files"
git push --set-upstream origin modular/command_script
history
cd NEAT-work/
git branch -a
git checkout -b command_script
ls
clear
git status
git add *
git commit -m "adding command_script files"
git push
#
cd /home/suvinit
rm -rf NEAT-work
git clone [email protected]:VarenyaJ/NEAT-work.git
cd NEAT-work
git fetch
git checkout -b modular/command_script
#manually add files
git status
git add -A
git commit -m "added some modularization files"
git push --set-upstream origin modular/command_script
git config http.postBuffer 524288000
cat ~/.ssh/config
#edit manually
touch sequential-git_push.sh
vim sequential-git_push.sh
cp sequential-git_push.sh local-push-split.sh
chmod +x local-push-split.sh
cp local-push-split.sh /home/suvinit/Desktop/
git push origin main --force
git config http.postBuffer 524288000
git push origin main --force
#git garbage collection
git gc
git gc --aggressive
git config http.postBuffer 2147483648
git push origin main --force
git status
git add * && git commit -m "Adding old BLAST files"
git push
git config http.postBuffer 1048576000
git config http.lowSpeedLimit 0
git config http.lowSpeedTime 999999
cat .git/config
git status
git push origin main --force
git add sequential-git_push.sh && git commit -m "scipt to possibly split git pushes and packs into smaller chunks. Since <pack.packSizeLimit> does not affect pushes, only repacking, this may or may not work"
#
git log
git reset --soft HEAD~1
git status
git reset --soft HEAD~1
git status
cd /home/suvinit && rm -rf NEAT-work && git clone [email protected]:VarenyaJ/NEAT-work.git && cd /home/suvinit/NEAT-work && cp /home/suvinit/Desktop/git-stuff /home/suvinit/NEAT-work/ && git status
git commit -m "Adding some Modular refactored files for NEAT. Also adding a scipt to possibly split git pushes and packs into smaller chunks. Since <pack.packSizeLimit> does not affect pushes, only repacking, this may or may not work."
git push
cd /home/suvinit/NEAT-work/
cp /home/suvinit/Desktop/git-stuff /home/suvinit/NEAT-work/
git add git-stuff
git commit -m "adding some git commands I used"
git push
#
#to update to python 3.9:
#sudo apt update -y && sudo apt install python3.9 -y
#if <python3 --versison> still returns 3.8, try:
#create a list of update alternatives, first adding the old version to the list with the command
#sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.[old-version] 1
#then add the new verson:
#sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.9 2
#to configure the priority status of the versions:
#sudo update-alternatives --config python3
#The output displays the available choices and their assigned number.
#Type the number of the the version you want and press <Enter>
#
cd /home/suvinit/Desktop
./updatethingies.sh
sudo ap
cd /home/suvinit/Downloads
chmod +x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh
cd /home/suvinit/NEAT
git checkout modular/command_script
conda deactivate
conda env create -f environment.yml -n neat
conda activate neat
conda update -n base -c defaults conda
conda info --envs
conda activate neat
poetry install
conda install poetry
pip install dist/neat*whl --force-reinstall
python -m neat -help
conda deactivate
git pull origin feature/modularization
conda deactivate
conda env remove -n neat
cp environment.lock environment.yaml
conda env create -f environment.yaml -n neat
conda deactivate
git pull origin feature/modularization
cd /home/suvinit/miniconda3/envs/ && rm -rf neat/
pip install poetry
cd /home/suvinit/NEAT && conda env remove -n neat && conda env create -f environment.yml -n neat && conda activate neat
neat --help
python -m neat --help
conda deactivate
conda env remove -n neat
pip uninstall neat
conda env create -f environment.yml -n neat
conda update --all
git diff feature/modularization modular/command_script
conda deactivate
rm -rf dist/
git add *
git commit -m "tried fixing environment errors"git push
cd /home/suvinit/NEAT
mv /home/suvinit/NEAT/neat/cli/read_simulator_cli.py /home/suvinit/Desktop
mv -rf /home/suvinit/NEAT/testing_command_script /home/suvinit/testing_command_script
conda activate neat
neat --help
neat read_simulator_cli
neat read_simulator_cli -help
neat read_simulator_cli --help
conda config --set auto_activate_base false
#Add <conda deactivate> to the end of ~/.bashrc
clear && git status && git fetch && git branch && git add neat/cli/commands/read_simulator_cli.py neat.cfg && git commit -m "trying to fix environment again" && git push
clear && cd /home/suvinit/NEAT-work && git status && git branch -a
clear && git checkout modular/command_script && git status && ls neat/cli/commands/
cp /home/suvinit/NEAT/neat/cli/commands/read_simulator_cli.py /home/suvinit/NEAT-work/neat/cli/commands/
cp /home/suvinit/NEAT/neat.cfg /home/suvinit/NEAT-work/neat.cfg
clear && git status && git add neat/cli/commands/read_simulator_cli.py neat.cfg && git commit -m "trying to fix environment again" && git push
clear && cd /home/suvinit/NEAT-work && git checkout main && cp /home/suvinit/Desktop/git-stuff /home/suvinit/NEAT-work/
clear && git status && git add git-stuff && git commit -m "adding some git commands I used" && git push
#
conda deactivate && conda env remove -n neat && rm -rf /home/suvinit/miniconda3/envs/neat && rm -rf /home/suvinit/miniconda3/envs/neat && cd
cd && rm -rf NEAT && git clone [email protected]:ncsa/NEAT.git && cd /home/suvinit/NEAT
git checkout modular/command_script
#
#git add * && git commit -m "Adding Josh's edits" && git push
#
conda env create -f dev-environment.yml -n neat
conda activate neat
poetry install
neat --help
neat read_simulator_cli --help
rm neat.cfg && clear && neat read_simulator_cli -r /home/suvinit/NEAT-data/H1N1/H1N1.fa -R 150 -o /home/suvinit/NEAT/
#
#
#
}
################