File: Makefile

package info (click to toggle)
trinityrnaseq 2.11.0%2Bdfsg-6
  • links: PTS, VCS
  • area: main
  • in suites: bookworm, bullseye, sid
  • size: 417,528 kB
  • sloc: perl: 48,420; cpp: 17,749; java: 12,695; python: 3,124; sh: 1,030; ansic: 983; makefile: 688; xml: 62
file content (21 lines) | stat: -rw-r--r-- 1,739 bytes parent folder | download
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
test:
	${TRINITY_HOME}/Analysis/DifferentialExpression/PtR -m candidate.Trinity_trans.TMM.EXPR.matrix -s candidate.samples.txt --log2 --heatmap --heatmap_colorscheme 'black,yellow'
	${TRINITY_HOME}/Analysis/DifferentialExpression/PtR -m candidate.Trinity_trans.TMM.EXPR.matrix -s candidate.samples.txt --log2 --sample_cor_matrix
	${TRINITY_HOME}/Analysis/DifferentialExpression/PtR -m candidate.Trinity_trans.TMM.EXPR.matrix -s candidate.samples.txt --log2 --prin_comp 3 --add_prin_comp_heatmaps 5 --Zscale
	${TRINITY_HOME}/Analysis/DifferentialExpression/PtR -m candidate.Trinity_trans.TMM.EXPR.matrix -s candidate.samples.txt --compare_replicates
	${TRINITY_HOME}/Analysis/DifferentialExpression/PtR -m candidate.Trinity_trans.TMM.EXPR.matrix -s candidate.samples.txt --log2 --imgfmt svg --boxplot_log2_dist 0.8
	${TRINITY_HOME}/Analysis/DifferentialExpression/PtR -m candidate.Trinity_trans.TMM.EXPR.matrix -s candidate.samples.txt --log2 --top_variable_genes 300 --min_across_ANY_samples_gene_expr_val 5 --gene_cor_matrix
	${TRINITY_HOME}/Analysis/DifferentialExpression/PtR -m candidate.Trinity_trans.TMM.EXPR.matrix -s candidate.samples.txt --log2 --mean_vs_sd
#	head -n11 candidate.Trinity_trans.TMM.EXPR.matrix > test.matrix && ${TRINITY_HOME}/Analysis/DifferentialExpression/PtR -m test.matrix -s candidate.samples.txt --per_gene_plots --per_gene_plots_incl_vioplot

	${TRINITY_HOME}/Analysis/DifferentialExpression/PtR -m candidate.Trinity_trans.TMM.EXPR.matrix -s candidate.samples.txt --log2 --heatmap --heatmap_colorscheme 'black,yellow' --order_columns_by_samples_file

	touch ./test


clean:
	rm -f ./candidate.Trinity_trans.TMM.EXPR.matrix.*
	rm -f ./test
	rm -f ./test.matrix ./test.matrix.*
	rm -f ./*.pdf
	rm -f ./*.svg