Shell scripting (Bash, awk, sed), Unix utilities, file handling, string manipulation, and command-line tools.
BAM files store aligned sequence reads in a compressed binary format. Counting reads by chromosome is a common task in genomics workflows—useful for quality control, coverage analysis, and identifying potential sequencing biases. Using samtools idxstats The fastest and most straightforward approach is samtools idxstats, which requires an indexed BAM file: samtools index reads.bam samtools idxstats…
If you’re managing academic references, you need a tool that integrates seamlessly into your workflow. Here are the most practical open-source and free options available. Zotero Zotero is the strongest choice for researchers who want full control over their data. It’s open source, maintained by a nonprofit, and doesn’t require subscription fees. Core features: Browser…
When a Bash script spawns child processes—say script A starts B, which starts C, which runs rsync—you need a way to terminate the entire process tree cleanly. Simply killing the parent leaves orphaned children running in the background. The most reliable approach uses session IDs (SID). By default, child processes inherit the same session ID…
By default, Git doesn’t automatically configure your local branch to track its remote counterpart. You need to explicitly set up this tracking relationship so that git pull and git push know which remote branch to synchronize with. Setting Up Tracking for an Existing Branch If you already have a local branch and want it to…
If you need to scan documents on Windows, several solid open-source options exist. Here are the most practical choices. NAPS2 (Not Another PDF Scanner 2) NAPS2 remains the top recommendation for Windows scanning. It’s straightforward, actively maintained, and handles most scanner hardware without headaches. What it does: Scans from WIA and TWAIN-compatible scanners Saves to…
The standard crontab -e command opens an interactive editor, which doesn’t work in automated scripts. To add crontab entries non-interactively, you need to pipe a list of cron jobs directly to crontab -. Basic approach The simplest method reads the existing crontab, appends your new entry, and writes it back: (crontab -l 2>/dev/null; echo “@reboot…
The sed stream editor is the go-to tool for deleting lines from files in Linux. It’s fast, works on large files without loading everything into memory, and handles complex patterns easily. Delete a Single Line by Line Number To delete the 4th line from a file: sed -i ‘4d’ ./file The -i flag edits the…
Merging branches is one of the most common Git workflows. The basic process is straightforward, but understanding the different merge strategies and when to use them prevents silent mistakes and keeps your history clean. The Basic Merge Flow To merge a feature branch into another branch: git checkout rc git merge dev-harry This checks out…
Logging connections that hit rate-limit rules helps you identify brute force attempts and troubleshoot legitimate clients that are being blocked. The standard approach is to create a dedicated chain that logs packets before dropping them. Create a logging and drop chain First, create a custom chain to handle logging and dropping: iptables -N LOGNDROP iptables…
Rate-limiting SSH brute-force attempts is essential for any server exposed to the internet. Using iptables with the recent module, you can drop connections from IPs that exceed a threshold in a given time window—for example, blocking IPs that attempt more than 6 connections in 60 seconds. Using iptables The recent module tracks connection attempts by…
When you create a new branch locally and try to git pull, you’ll hit this error if the branch doesn’t have upstream tracking configured: You asked me to pull without telling me which branch you want to merge with, and ‘branch.dev-harry.merge’ in your configuration file does not tell me, either. This happens because Git doesn’t…
When backing up with rsync, you often need to skip directories like cache/, node_modules/, or .git/ that appear at multiple levels in your directory tree. Listing every instance individually is impractical, but rsync’s exclude patterns handle this elegantly. Basic exclude syntax The simplest approach uses –exclude with a directory name pattern: rsync -avxP –exclude=cache/ /path/to/src/directory/…
fdisk -l displays partition information in sectors by default, which isn’t practical for most sysadmin tasks. While fdisk itself lacks options to change the unit display, parted shows partition sizes in GB/MB/KB automatically and is the better tool for this job. Using parted for readable partition output Run parted with the -l flag to list…
When you need to change the commit message of a past commit that isn’t HEAD, git commit –amend alone won’t help. You’ll need to use interactive rebase to stop at that commit, amend it, and then continue. Interactive Rebase to Edit a Commit The core approach is git rebase -i with the commit hash. Say…
When working with codebases that use non-standard file extensions for C source files, ctags won’t recognize them by default. You can configure it to treat files with custom extensions like .c0 or .puc as C source code. Using the langmap option The simplest approach is to add language mappings to your ctags configuration. Edit ~/.ctags…
When working with non-standard C file extensions, Vim’s taglist plugin and filetype detection won’t automatically recognize them. You need to explicitly tell Vim to treat those files as C source. Basic approach Add this to your ~/.vimrc: autocmd BufRead,BufNewFile *.c0 set filetype=c Replace *.c0 with whatever extension you’re using. This tells Vim that any file…
When you SSH to a server and see the warning below, your SSH client has detected that the server’s host key doesn’t match what’s stored locally: @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ @ WARNING: REMOTE HOST IDENTIFICATION HAS CHANGED! @ @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ IT IS POSSIBLE THAT SOMEONE IS DOING SOMETHING NASTY! Someone could be eavesdropping on you right now (man-in-the-middle attack)!…
The replication factor determines how many copies of each data block HDFS maintains across your cluster. The default is 3, which provides adequate fault tolerance for most deployments by surviving both node and rack failures simultaneously. Setting Cluster-Wide Default Replication To set the default replication factor for all new files, add the dfs.replication property to…
When you need to reach a server through one or more intermediate hosts, you can establish a direct connection without manually chaining SSH sessions. This is essential for accessing internal servers that aren’t directly reachable from your workstation. The scenario laptop —-> proxy —-> server You want to connect to server.example.com through proxy.example.com as if…
The @ symbol in Makefiles suppresses the echo of the command itself before execution. When you run a target, make normally prints each command to stdout before running it. Adding @ before a command hides that echo, showing only the command’s output. Basic example Without @: all: echo “For correctness test of basic get and…