deleted autogenerated scripts

Planemo.sh

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+
+
+
+
+
+
+conda create -y --quiet --use-local --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --name __fleeqtk@1.3 fleeqtk=1.3
+ # or
+conda create --use-local --name __fleeqtk@1.3 fleeqtk=1.3
+
+ # check if env is created
+ls ~/miniconda3/envs/
+
+planemo test --conda_use_local fleeqtk_seq.xml

irod.sh

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+wget -qO - https://packages.irods.org/irods-signing-key.asc | sudo apt-key add -
+echo "deb [arch=amd64] https://packages.irods.org/apt/ $(lsb_release -sc) main" | sudo tee /etc/apt/sources.list.d/renci-irods.list
+sudo apt-get update  # this primes the system for installation
+
+sudo apt-get install irods-icommands # installs 
+
+iinit # initialise for log in details 
+ils  # iplant version of ls
+
+iput -rPT Documents/hello_world/test-data /iplant/home/dave_k/ # upload directory (bulk upload) directly to home directory in cyverse
+
+icp /iplant/home/mukani/analyses/tutorial_data.csv /iplant/home/dave_k/ # iplant version of coy from one folder to another in cyverse
+
+iget -Pf /iplant/home/dave_k/Ordered_snp_allele.csv # download file from path in cyverse to path in curent shell
+
+ils -l | awk '{ print $7 " " $4 }' # print the name nd size of file

network_cmd.bash

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+
+for ((i=1;i<=100;i++));do echo foo$i; sleep 1;done 
+for ((i=1;i<100;i++)); do echo foo$i; sleep 1; done
+
+sudo adduser --home /home/<username> <username> # create use
+
+sudo chown -R beca-09:beca-09 .ssh/ # change permissions to vm 
+
+ssh-keygen -t rsa # generate key for successful login
+
+# copy the .pub key from the patner into the last entry in authorised-key file.
+
+ssh <username>@<ip_address> # way to ssh to user
+ssh -i .ssh/authorized_keys beca-11@10.0.72.60
+
+##
+sudo mkdir /home/<newuser>/<.ssh>  # create a new file in users directory
+sudo vi /home/<newuser>/<.ssh>/<authorized_keys> # create key file for user to successfully login
+
+sudo usermod -aG sudo <newuser> # allow newuser to be su
+
+# now to docker
+sudo apt-get update # Update the apt package index:
+
+sudo apt-get install apt-transport-https ca-certificates curl software-properties-common  # Install packages to allow apt to use a repository over HTTPS:
+
+curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add - # Add Docker’s official GPG key
+
+sudo apt-key fingerprint 0EBFCD88 # Verify that you now have the key with the fingerprint last 8 digits
+
+sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable" # set up the stable repository
+
+sudo apt-get update # Update the apt package index.
+
+sudo apt-get install docker-ce # Install the latest version of Docker CE
+
+sudo docker run hello-world # Verify that Docker CE is installed correctly by running the hello-world image.
+
+sudo docker run docker/whalesay cowsay "$(fortune)" # second test
+
+sudo usermod -aG docker beca-09 # add docker to su group
+
+docker run -ti centos # run latest centos image
+
+docker run -ti centos:7 # run centos 7 image
+
+docker start <container_id> # start the container saved
+
+docker attach <container_id> # load the started container
+
+docker commit mysoft1 centoswith # save the container as image with files and changes
+
+docker run --volume myfirstvol:/root/newfolder -ti centos:7 # create a volume using centos
+# touch /root/newfolder/docvol.txt
+
+sudo su - # turn to root user 
+
+cat /var/lib/docker/volumes/myfirstvol/_data/docvol.txt # view the file created in volume cmd above
+
+docker run --volume myfirstvol:/root/newfolder2:ro -ti centos # load a read only folder/file 
+
+# a docker file needs to be named .docker 
+		# the centos base image
+		FROM centos:7
+
+		# labels
+		LABEL centos.version="7"
+
+		# apps to install
+
+		RUN yum -y update && yum -yy install vim
+		RUN useradd beca-09
+		ADD <url_of_file_to_be_used> <location/where/to/be/downloaded> # will be created if non-existent
+
+		USER beca-09
+		# the working directory
+		WORKDIR /home/
+
+docker build -t vimimage .
+
+		#entry point addition to the docker file
+
+		ENTRYPOINT ["/bin/echo", "hello world!"]
+
+
+docker build -t vimimagecho . # build new image
+
+docker run vimimagecho # run new image
+
+docker run --entrypoint "/bin/which" entrypoint ls # to modify the entrypoint executable
+
+docker run -ti --entrypoint "/bin/bash" vimimagecho # to run the image interactively
+
+ echo $null >Dockerfile # empty the file
+
+docker ps -aq -f status=exited # list all exited containers
+
+docker ps -aq --no-trunc -f status=exited | xargs docker rm # Remove stopped containers
+
+docker ps --since 6bb20a720eb4 -q | xargs docker rm #Remove containers created after a specific container
+
+ Rscript 100_tree.R # in the container
+
+ docker rmi --force <IMAGEID> # to forcefully remove an image as well as the attached containers 

soap_allign_hpc.bash

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+samtools tview SRR3134441_tr.bam ../Map/Zea_mays.AGPv4.dna.toplevel.fa
+for f in *; do echo "Processing ${f}"; module load samtools; samtools index ${f};done
+#### vim script for creating a soap index
+#!/bin/bash
+#SBATCH -J soap_indexing
+#SBATCH -p batch
+#SBATCH -n 4
+#SBATCH --mail-user=DKaimenyi@cgiar.org
+#SBATCH -o ./soap_index.%N.%j.out
+#SBATCH -e ./soap_index.%N.%j.err
+#SBATCH --mail-type=END,FAIL
+
+cd /home/dkiambi/reads/new_map
+
+module load SOAPaligner/2.21
+
+2bwt-builder ./Zea_mays.AGPv4.dna.toplevel.fa -p 10
+
+###multiple jobs
+#!/bin/bash
+#SBATCH -J soap_map_41_un_dave
+#SBATCH -p batch
+#SBATCH -n 4
+#SBATCH --mail-user=D.Kaimenyi@cgiar.org
+#SBATCH -o ./soap_map_utr_41.%N.%j.out
+#SBATCH -e ./soap_map_untr_41.%N.%j.err
+#SBATCH --mail-type=END,FAIL
+
+cd /home/dkiambi/reads
+
+module purge
+
+module load SOAPaligner/2.21
+
+soap -D ./new_map/Zea_mays.AGPv4.dna.toplevel.fa.index -a ./reads/SRR3134441/SRR3134441_1.fastq.gz -b ./reads/SRR3134441/SRR3134441_2.fastq.gz -o ./SRR3134441_unt_soap.txt -2 ./SRR3134441_unt_soap_unpaired.txt -M 4 -p 10
+
+for f in *.sh; do echo "submitting ${f}"; sbatch ${f};done
+
+# viewing allingment
+cd /var/scratch/Dave/Exercise/reads/
+module load tablet
+tablet
+## blast workthrough
+module load blast
+makeblastdb -in Exercise/reads/Map/Zea_mays.AGPv4.dna.toplevel.fa -dbtype nucl
+blastn -query GW2_rice.fa -db Exercise/reads/Map/Zea_mays.AGPv4.dna.toplevel.fa -out maize_blast.txt -evalue 0.00001 -outfmt 7
+
+blastx -query GW2_rice.fa -db nr -out gw2_blastx.txt -num_threads 10 -max_target_seqs 20 -best_hit_score_edge 0.25
+
+## Generating fasta statistics for downloaded genomes 
+for f in ./*; do echo "processing ${f}"; module load seqkit/0.7.2; seqkit stats ${f}; done
+