Command Log: September 24, 2024, 9:34 am

pwd
ls 
unzip shell-lesson-data.zip
ls 
ls -F 
ls -F shell-lesson-data
ls -F shell-lesson-data/exercise-data/
man ls
man ls
pwd
ls
cd shell-lesson-data/exercise-data/alkanes/
ls -lthr
ls -aF
cd ..
pwd
ls -F
cd -
mkdir -p test1/test2
ls -F
ls -F test1/
rm -i octane.pdb 
ls
ls *.pdb
ls *pane
ls *p*
ls *pan*
ls *t?ane*
touch test.txt
ls
nano test2.txt
cat test2.txt 
cat cubane.pdb
head -n cubane.pdb
head cubane.pdb
head -n 5 cubane.pdb
head -n 5 cubane.pdb|tail -n 3 
head -n 5 cubane.pdb|tail -n 3 >>middle_data
ls
cat middle_data 
head -n 5 cubane.pdb|tail -n 3 > middle_data
cat middle_data 
head -n 5 cubane.pdb|tail -n 3 >> middle_data
cat middle_data 
ls -F
nano middle.sh
cat middle.sh 
ls -F
chmod +x middle.sh 
ls -F
bash middle.sh 
cat middle.sh 
nano middle.sh 
cat middle.sh 
bash middle.sh 
bash middle.sh propane.pdb
nano middle.sh 
cat middle.sh 
bash middle.sh propane.pdb
bash middle.sh propane.pdb 7 3
cat middle.sh 
pwd
cat middle.sh 
nano middle.sh
bash middle.sh propane.pdb 7 3
cat middle.sh 
ls
pwd
wc cubane.pdb
wc -l cubane.pdb
wc *.pdb
wc -l *.pdb
wc -l *.pdb >> lengths.txt
cat lengths.txt 
sort lengths.txt 
sort -n lengths.txt 
cat lengths.txt 
wc -l lengths.txt 
head -n 6 lengths.txt > lengths.txt 
cat lengths.txt 
wc -l *.pdb|head -n 6 >> lengths.txt 
cat lengths.txt 
sort -n lengths.txt 
sort -nr lengths.txt 
wc -l *.pdb|sort -nr|head -n 1
wc -l *.pdb|sort -nr|head -n 2|tail -n 1
pwd
cd ../animal-counts/
ls
cd ..
ls
cd creatures/
ls
cat basilisk.dat 
head -n 5 basilisk.dat 
ls -F
head -n 5 *.dat
nano loop_example
ls -f
ls -F
chmod +x loop_example
ls -F
./loop_example 
cat loop_example 
nano loop_example
./loop_example 
nano loop_example
nano loop_number.sh
chmod +x loop_number.sh 
ls -F
./loop_number.sh 
nano loop_number.sh
./loop_number.sh 
nano loop_number.sh
./loop_number.sh 
nano loop_number.sh
./loop_number.sh 
nano loop_number.sh
./loop_number.sh 
nano loop_number.sh
./loop_number.sh 
cat loop_number.sh 
cat loop_number.sh 
cat loop_example 
cd ../alkanes/
ls
nano multi_variable.sh
chmod +x multi_variable.sh 
ls -F
./multi_variable.sh cubane.pdb propane.pdb 
./multi_variable.sh cubane.pdb 
./multi_variable.sh cubane.pdb propane.pdb methane.pdb
./multi_variable.sh *.pdb
ls
cd ../writing/
ls
cat haiku.txt 
grep not haiku.txt 
grep The haiku.txt 
grep -w The haiku.txt 
grep -n "it" haiku.txt
grep -c "it" haiku.txt
grep -i The haiku.txt
grep -r Yesterday .
grep -rc Yesterday .
grep -E "^.o" haiku.txt
find .
cd ..
ls
find .
find 
find . -type d
find . -type f
find . -name "*.txt"
wc -l $(find . -name "*.txt")
wc -l $(find . -name "*.txt")| sort -n
find . -type d -empty
clear
pwd
clear
ls /work/HCC/BCRF/
ls /work/HCC/BCRF/indices/
ls /work/HCC/BCRF/indices/bowtie2/
ls /work/HCC/BCRF/indices/bowtie2/Bacillus_subtilis_168/
ls /work/HCC/BCRF/indices/bowtie2/Bacillus_subtilis_168/Ensembl/
ls /work/HCC/BCRF/indices/bowtie2/Bacillus_subtilis_168/Ensembl/EB2/
clear
cd $WORK
pwd
mkdir nf-training
cd nf-training/
cp /work/demo/hccdemo/public/environment.yml .
ls
srun --qos=short --mem=5gb --time=02:00:00 --pty $SHELL
srun --qos=short --mem=5gb --time=02:00:00 --pty $SHELL
srun --qos=short --mem=5gb --time=02:00:00 --pty $SHELL
module purge
module load miniforge nano
mamba env create -n nf-training -f environment.yml​
ls
more environment.yml 
mamba env create -n nf-training -f environment.yml 
conda clean -y all
conda clean -y -all
rm -rf $WORK/.conda/
rm -rf $WORK/.conda/
rm -rf $WORK/.conda/
rm -rf $WORK/.conda/
rm -rf $WORK/.conda/
rm -rf $HOME/.conda/envs/nf-training/
srun --qos=short --mem=15gb --time=02:00:00 --pty $SHELL