Merge branch 'dev' of /home/kai.b/tools/universc (e60c20af) · Commits · github_fork / Universc

Dockerfile

+11 −0

Original line number	Diff line number	Diff line
		@@ -65,6 +65,17 @@ RUN git clone https://github.com/linsalrob/fastq-pair.git \
		&& gcc -std=gnu99 ../main.c ../robstr.c ../fastq_pair.c ../is_gzipped.c -o fastq_pair \
		&& cp fastq_pair /bin/fastq_pair

		# Install STAR aligner
		RUN wget https://github.com/alexdobin/STAR/archive/2.5.1b.tar.gz \
		&& tar -xf 2.5.1b.tar.gz \
		&& rm 2.5.1b.tar.gz \
		&& cd STAR-2.5.1b \
		&& make \
		&& mv bin/Linux_x86_64/STAR* /usr/bin \
		&& cd source \
		&& make \
		&& cd /

		# RUN wget https://sourceforge.net/projects/bbmap/files/latest/download ; mv download BBMap_38.87.tar.gz \
		# && tar -xvzf BBMap_38.87.tar.gz

launch_universc.sh

+5 −6

Original line number	Diff line number	Diff line
		@@ -207,9 +207,9 @@ Mandatory arguments to long options are mandatory for short options too.
		C1 RamDA-Seq (16 bp, No UMI): c1-ramda-seq
		CEL-Seq (8 bp barcode, 4 bp UMI): celseq
		CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2
		Drop-Seq (12 bp barcode, 8 bp UMI): dropseq
		Drop-Seq (12 bp barcode, 8 bp UMI): dropseq, nadia
		ICELL8 3′ scRNA version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2
		ICELL8 3′ scRNA version 3 (11 bp barcode, 14 bp UMI): icell8 or custom
		ICELL8 3′ scRNA version 3 (11 bp barcode, 14 bp UMI): icell8
		ICELL8 5′ scRNA with TCR OR kit (10bp barcode, NO bp UMI): icell8-5-prime
		ICELL8 full-length scRNA with Smart-Seq (16 bp barcode, No UMI): icell8-full-length
		inDrops version 1 (19 bp barcode, 6 bp UMI): indrops-v1, 1cellbio-v1
		@@ -225,7 +225,7 @@ Mandatory arguments to long options are mandatory for short options too.
		RamDA-Seq (16 bp barcode, no UMI): ramda-seq
		SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2
		SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3
		SCIFI-Seq (27 bp barcode, 8 bp UMI
		SCIFI-Seq (27 bp barcode, 8 bp UMI): scifiseq
		SCRB-Seq (6 bp barcode, 10 bp UMI): scrbseq, mcscrbseq
		SeqWell (12 bp barcode, 8 bp UMI): plexwell, seqwell, seqwells3
		Smart-seq (16 bp barcode, No UMI): smartseq
		@@ -257,8 +257,7 @@ Mandatory arguments to long options are mandatory for short options too.
		-p, --per-cell-data Generates a file with basic run statistics along with per-cell data

		--non-umi or --read-only Force counting reads by adding or replacing UMI with a mock sequence.
		Available for: ICELL8, Smart-Seq2
		Default for: Quartz-Seq, RamDA-Seq, Smart-Seq, Smart-Seq2, STRT-Seq
		Default for: Quartz-Seq, RamDA-Seq, Smart-Seq, Smart-Seq2, STRT-Seq, ICELL8 3-prime version2

		--setup Set up whitelists for compatibility with new technology and exit
		--as-is Skips the FASTQ file conversion if the file already exists

sub/MakeNewReference.pl

+17 −0

Original line number	Diff line number	Diff line
		@@ -29,6 +29,7 @@ my $name = "";

		#making the options into external arguments.
		GetOptions (
		<<<<<<< HEAD
		'genome=s' => \$genome,
		'annotation=s' => \$annotation,
		'name=s' => \$name
		@@ -43,6 +44,22 @@ elsif (!$annotation){
		}
		elsif (!$name) {
		die "USAGE: option --name <reference name> is required.\n";
		=======
		'genome=s' => \$genome,
		'annotation=s' => \$annotation,
		'name=s' => \$name
		);

		#checking for sequence type
		if (!$genome) {
		die "USAGE: option --genome <FASTA file> is required.\n";
		}
		elsif (!$annotation){
		die "USAGE: option --annotation <GTF file> is required.\n";
		}
		elsif (!$name) {
		die "USAGE: option --name <reference name> is required.\n";
		>>>>>>> 4957925f3efbae4b8c2328ab7f351fc66469be60
		}

		print "check complete.\n\n";

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