Command line exercise solutions
The pwd commands in these solutions are added to clarify the working directories used.
1. Change the working directory from bioinfo-notebook/ to bioinfo-notebook/data/.
ronan@dell:~/bioinfo-notebook$ pwd
/home/ronan/bioinfo-notebook
ronan@dell:~/bioinfo-notebook$ cd data/
ronan@dell:~/bioinfo-notebook/data$ pwd
/home/ronan/bioinfo-notebook/data
2. Change the working directory from bioinfo-notebook/data to bioinfo-notebook/docs, using ../ in your command.
ronan@dell:~/bioinfo-notebook/data$ pwd
/home/ronan/bioinfo-notebook/data
ronan@dell:~/bioinfo-notebook/data$ cd ../docs/
ronan@dell:~/bioinfo-notebook/docs$ pwd
/home/ronan/bioinfo-notebook/docs
3. List the files in the bioinfo-notebook/docs/ directory.
ronan@dell:~/bioinfo-notebook/docs$ pwd
/home/ronan/bioinfo-notebook/docs
ronan@dell:~/bioinfo-notebook/docs$ ls
bowtie2.md file_formats.md
bowtie.md htseq-count.md
cl_intro.md linux_setup.md
cl_solutions.md part1.md
combining_featCount_tables.md part2.md
conda.md part3.md
fasterq-dump.md samtools.md
fastq-dump.md to_do.md
fastq-dump_to_featureCounts.md ubuntu_virtualbox.md
featureCounts.md wsl.md
4. Select a file in the bioinfo-notebook/docs/ directory, and display the first 6 lines of it using the head command.
ronan@dell:~/bioinfo-notebook/docs$ pwd
/home/ronan/bioinfo-notebook/docs
ronan@dell:~/bioinfo-notebook/docs$ head cl_solutions.md
---
layout: default
title: Command line exercise solutions
nav_exclude: true
---
# Command line exercise solutions
1. Change the working directory from `bioinfo-notebook/` to `bioinfo-notebook/data/`.
5. Display the last 2 lines of all the files in the bioinfo-notebook/docs/ directory, using the tail command.
ronan@dell:~/bioinfo-notebook/docs$ pwd
/home/ronan/bioinfo-notebook/docs
ronan@dell:~/bioinfo-notebook/docs$ tail -n 2 *
==> bowtie2.md <==
1. The `bowtie2` manual: <http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml>
==> bowtie.md <==
1. The `bowtie` manual: <http://bowtie-bio.sourceforge.net/manual.shtml>
==> cl_intro.md <==
- [File formats used in bioinformatics](/bioinfo-notebook/docs/file_formats.html)
- [The DataCamp "Introduction to Shell" interactive course](https://www.datacamp.com/courses/introduction-to-shell-for-data-science)
==> cl_solutions.md <==
5. Display the last 2 lines of all the files in the `bioinfo-notebook/docs/` directory, using the `tail` command.
6. From the `bioinfo-notebook/docs/` directory, list the files in the `bioinfo-notebook/envs/` directory.
==> combining_featCount_tables.md <==
- [fastq-dump_to_featureCounts.sh](/bioinfo-notebook/docs/fastq-dump_to_featureCounts.html)
==> conda.md <==
2. Conda packages: <https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/packages.html>
3. Conda environments: <https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/environments.html>
==> fasterq-dump.md <==
1. [How to use fasterq-dump from the sra-tools wiki on GitHub](https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump)
==> fastq-dump.md <==
1. Rob Edward's notes on `fastq-dump`: <https://edwards.sdsu.edu/research/fastq-dump/>
==> fastq-dump_to_featureCounts.md <==
1. [fastq-dump_to_featureCounts.sh on GitHub](https://github.com/rnnh/bioinfo-notebook/blob/master/scripts/fastq-dump_to_featureCounts.sh)
==> featureCounts.md <==
1. The `subread` user guide: <http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf>
2. The `featureCounts` paper: <https://doi.org/10.1093/bioinformatics/btt656>
==> file_formats.md <==
- [GTF2.2: A Gene Annotation Format (Revised Ensembl GTF)](http://mblab.wustl.edu/GTF22.html)
- [GFF3 Specification](https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md)
==> htseq-count.md <==
1. The `htseq-count` manual: <https://htseq.readthedocs.io/en/release_0.11.1/count.html>
==> linux_setup.md <==
- [Using Ubuntu through a Virtual Machine](/bioinfo-notebook/docs/ubuntu_virtualbox.html)
- [Windows Subsystem for Linux](/bioinfo-notebook/docs/wsl.html)
==> part1.md <==
These are general guides for installing Ubuntu, using the command line, and the types of files used in bioinformatics.
==> part2.md <==
These are guides to individual programs.
==> part3.md <==
These are scripts that use the programs discussed in this project.
==> samtools.md <==
- [Alignment formats](/bioinfo-notebook/docs/file_formats.html#alignment-formats)
- The `samtools` manual: <https://www.htslib.org/doc/samtools.html>
==> to_do.md <==
- Add page on `trimmomatic`
- Entry on BED/bigWig
==> ubuntu_virtualbox.md <==
- [What is a Virtual Machine?](https://azure.microsoft.com/en-us/overview/what-is-a-virtual-machine/)
- [How to Install Ubuntu on VirtualBox](https://www.wikihow.com/Install-Ubuntu-on-VirtualBox)
==> wsl.md <==
- [Using Ubuntu through a Virtual Machine](/bioinfo-notebook/docs/ubuntu_virtualbox.html)
- [conda](/bioinfo-notebook/docs/conda.html)
6. From the bioinfo-notebook/docs/ directory, list the files in the bioinfo-notebook/envs/ directory.
ronan@dell:~/bioinfo-notebook/docs$ pwd
/home/ronan/bioinfo-notebook/docs
ronan@dell:~/bioinfo-notebook/docs$ ls ../envs/
bioinfo-notebook.txt bioinfo-notebook.yml