02[11:48] * calmar (~calmar@46-127-51-134.dynamic.hispeed.ch) Quit (Quit: Lost terminal)
[11:49] xargs sucks.
[11:50] moving files from /tmp/ to /tmp/ sucks too. rethink your strategy.
[11:51] !switch
[11:51] !case
[11:51] case word in pattern);; esac syntax is used to match a word against a particular pattern, and execute commands if that pattern matches. See ‘case word in’ in man bash | http://wiki.bash-hackers.org/syntax/ccmd/case
03[11:52] * Mo (c100f615@gateway/web/freenode/ip.193.0.246.21) has joined #bash
03[11:54] * bzinger (~bzinger@79.135.102.174) has joined #bash
03[11:55] * LordDoskias (~chichiman@unaffiliated/lorddoskias) has joined #bash
[11:55] !paste
[11:55] what’s the statement in bash that goes to the next loop iteration? continue or next?
[11:55] Please don’t waste our time by making us go to a pastebin just for a five-line snippet. Paste it in the channel. If you have a larger script that’s showing problems, trim it down to the bare minimum size that still shows the problem. You’ll probably fix it yourself once you do that.
[11:56] noc_, continue
02[11:56] * mkurz (~chatzilla@193.158.24.243) Quit (Quit: ChatZilla 0.9.87 [Firefox 3.6.16/20110323163108])
[11:56] spank you sir
[11:56] if [[ $readtype == "-shortPaired" ]]; then
[11:56] if [[ $filetype == "-fasta.gz" || $filetype == "-fastq.gz" ]]; then
[11:56] splitoutput=$(echo $source | tr «,» «\n»)
[11:56] filetype=$(echo $filetype | awk ‘sub(«.gz$», «»)’)
[11:56] for x in $splitoutput
[11:56] gunzip $x
[11:56] processed+=$(ls $x | awk ‘sub(«.gz$», «»)’)
[11:56] done
[11:56] fi
[11:56] if [[ $filetype == "-fasta" ]]; then
[11:57] /home/ec2-user/binaries/shuffleSequences_fasta.pl processed[0] processed[1] MERGED.fasta
[11:57] elif [[ $filetype == "-fastq" ]]; then
[11:57] /home/ec2-user/binaries/shuffleSequences_fasta.pl processed[0] processed[1] MERGED.fastq
[11:57] fi
[11:57] stop.
[11:57] fi
[11:57] ?
[11:57] /topic
[11:57] hey why isn’t there a pastebin in the topic?
[11:57] meh
[11:57] i read the topic
[11:57] that;s why i posted in the channel
[11:57] Because not everyone likes pastebins.
[11:58] you really weren’t able to find a pastebin of your own?
[11:58] well I’m pretty sure everyone hates people who paste into channels too. so what’s the solution?
02[11:58] * lesshaste (~lesshaste@87-194-206-189.bethere.co.uk) Quit (Quit: Leaving)
[11:58] http://pastebin.com/faFrh0E3
02[11:58] * superlinux (~oracle@unaffiliated/superlinux) Quit (Quit: I ♥ Palestine)
[11:58] scripts/merge_step: line 22: syntax error near unexpected token `gunzip’
[11:58] scripts/merge_step: line 22: ` gunzip $x’
[11:58] I guess I’m not part of everyone then.
[11:58] this is the error i get
03[11:59] * Kjellski (~kjellski@141.22.5.9) has joined #bash
[11:59] and i have no clue why
[11:59] you know what I mean, people in here complain about pastebins, don’t recommend one in the topic or channel message, and then when you paste 10 lines into the channel you’ll get yelled on for that too.
[11:59] LordDoskias: Your for is missing a do
03[11:59] * lixus (~lixus@h03.hostsharing.net) has joined #bash
[12:00] !quotes > LordDoskias
[12:00] LordDoskias: «USE MORE QUOTES!» They are vital. Also, learn the difference between ‘ and » and `. See and .
[12:00] !ls > LordDoskias
[12:00] LordDoskias: ls shows you a representation of files. They are NOT file names (for simple names, they mostly happen to be equivalent). Do NOT try to parse it. http://mywiki.wooledge.org/ParsingLs
03[12:00] * blackpenguin (~bp@unaffiliated/blackpenguin) has joined #bash
[12:00] And use array instead of string (splitoutput).
[12:01] i’ll be back in an hour
02[12:01] * Naib (~j@fu/hw/naib) Quit (Quit: Nothing to see here)
03[12:01] * Naib (~j@fu/hw/naib) has joined #bash
02[12:02] * nilg (~user@hst-138-109.cisbg.com) Quit (Read error: Connection reset by peer)
[12:02] anyway
[12:02] i thought that this is actually an array
03[12:02] * switch (~unknown@unaffiliated/switch) has joined #bash
[12:03] or should i change that to += ?
[12:03] strings don’t magically turn into arr
