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Enable better use of sub-make #2

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4 changes: 2 additions & 2 deletions test_SuperTranscript/Makefile
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test:
./runMe.sh
cd indiv_tests && make test
cd indiv_tests && $(MAKE) test
@touch test

clean:
./cleanMe.sh
cd indiv_tests && make clean
cd indiv_tests && $(MAKE) clean

3 changes: 2 additions & 1 deletion ..._and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_denovo.sh
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make TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/DROSOPHILA/10M/trinity_out_dir/Trinity.fasta SAMPLES=misc_tests/drosoph_denovo.samples.txt
MAKE=${MAKE:-make}
${MAKE} TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/DROSOPHILA/10M/trinity_out_dir/Trinity.fasta SAMPLES=misc_tests/drosoph_denovo.samples.txt
3 changes: 2 additions & 1 deletion ...ign_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_ref.sh
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make TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/DROSOPHILA/Annotations/Drosoph_coding.cdna SAMPLES=misc_tests/drosoph_ref.samples.txt
MAKE=${MAKE:-make}
${MAKE} TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/DROSOPHILA/Annotations/Drosoph_coding.cdna SAMPLES=misc_tests/drosoph_ref.samples.txt
3 changes: 2 additions & 1 deletion ...gn_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_denovo.sh
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make TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/MOUSE_RNASEQ_METHODS_ANALYSIS/10M/SS_trin_test/run_devel/trinity_out_dir/Trinity.fasta SAMPLES=misc_tests/mouse_denovo.samples.txt
MAKE=${MAKE:-make}
${MAKE} TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/MOUSE_RNASEQ_METHODS_ANALYSIS/10M/SS_trin_test/run_devel/trinity_out_dir/Trinity.fasta SAMPLES=misc_tests/mouse_denovo.samples.txt
3 changes: 2 additions & 1 deletion ...align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_ref.sh
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make TRINITY_FASTA=/seq/regev_genome_portal/RESOURCES/mouse/mm9/Annotations/mm9_ucsc_genomeStudio_genes/mm9_ucsc_genomeStudio_genes.gtf.trans.fa SAMPLES=misc_tests/mouse_ref.samples.txt
MAKE=${MAKE:-make}
${MAKE} TRINITY_FASTA=/seq/regev_genome_portal/RESOURCES/mouse/mm9/Annotations/mm9_ucsc_genomeStudio_genes/mm9_ucsc_genomeStudio_genes.gtf.trans.fa SAMPLES=misc_tests/mouse_ref.samples.txt
3 changes: 2 additions & 1 deletion ...n_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_denovo.sh
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make TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/SCHIZO_RNASEQ_METHODS_ANALYSIS/10M/SS_trin_test/run_devel_trinity/trinity_out_dir/Trinity.fasta SAMPLES=misc_tests/schizo_denovo.samples.txt
MAKE=${MAKE:-make}
${MAKE} TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/SCHIZO_RNASEQ_METHODS_ANALYSIS/10M/SS_trin_test/run_devel_trinity/trinity_out_dir/Trinity.fasta SAMPLES=misc_tests/schizo_denovo.samples.txt
3 changes: 2 additions & 1 deletion ...lign_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_ref.sh
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make TRINITY_FASTA=/home/unix/bhaas/utilities/schizo/SP2_GeneDB.290110.prot_coding.cds.nr SAMPLES=misc_tests/schizo_ref.samples.txt
MAKE=${MAKE:-make}
${MAKE} TRINITY_FASTA=/home/unix/bhaas/utilities/schizo/SP2_GeneDB.290110.prot_coding.cds.nr SAMPLES=misc_tests/schizo_ref.samples.txt
3 changes: 2 additions & 1 deletion ..._and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_denovo.sh
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make TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/DROSOPHILA/10M/trinity_out_dir/Trinity.fasta SAMPLES=drosoph.samples.txt
MAKE=${MAKE:-make}
${MAKE} TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/DROSOPHILA/10M/trinity_out_dir/Trinity.fasta SAMPLES=drosoph.samples.txt
3 changes: 2 additions & 1 deletion ...ign_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_ref.sh
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make TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/DROSOPHILA/Annotations/Drosoph_coding.cdna SAMPLES=misc_tests/drosoph_ref.samples.txt
MAKE=${MAKE:-make}
${MAKE} TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/DROSOPHILA/Annotations/Drosoph_coding.cdna SAMPLES=misc_tests/drosoph_ref.samples.txt
3 changes: 2 additions & 1 deletion ...gn_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_denovo.sh
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make TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/MOUSE_RNASEQ_METHODS_ANALYSIS/10M/SS_trin_test/run_devel/trinity_out_dir/Trinity.fasta SAMPLES=mouse.samples.txt
MAKE=${MAKE:-make}
${MAKE} TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/MOUSE_RNASEQ_METHODS_ANALYSIS/10M/SS_trin_test/run_devel/trinity_out_dir/Trinity.fasta SAMPLES=mouse.samples.txt
3 changes: 2 additions & 1 deletion ...align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_ref.sh
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make TRINITY_FASTA=/seq/regev_genome_portal/RESOURCES/mouse/mm9/Annotations/mm9_ucsc_genomeStudio_genes/mm9_ucsc_genomeStudio_genes.gtf.trans.fa SAMPLES=misc_tests/mouse_ref.samples.txt
MAKE=${MAKE:-make}
${MAKE} TRINITY_FASTA=/seq/regev_genome_portal/RESOURCES/mouse/mm9/Annotations/mm9_ucsc_genomeStudio_genes/mm9_ucsc_genomeStudio_genes.gtf.trans.fa SAMPLES=misc_tests/mouse_ref.samples.txt
3 changes: 2 additions & 1 deletion ...n_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_denovo.sh
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make TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/SCHIZO_RNASEQ_METHODS_ANALYSIS/10M/SS_trin_test/run_devel_trinity/trinity_out_dir/Trinity.fasta SAMPLES=schizo.samples.txt
MAKE=${MAKE:-make}
${MAKE} TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/SCHIZO_RNASEQ_METHODS_ANALYSIS/10M/SS_trin_test/run_devel_trinity/trinity_out_dir/Trinity.fasta SAMPLES=schizo.samples.txt
3 changes: 2 additions & 1 deletion ...lign_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_ref.sh
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make TRINITY_FASTA=/home/unix/bhaas/utilities/schizo/SP2_GeneDB.290110.prot_coding.cds.nr SAMPLES=misc_tests/schizo_ref.samples.txt
MAKE=${MAKE:-make}
${MAKE} TRINITY_FASTA=/home/unix/bhaas/utilities/schizo/SP2_GeneDB.290110.prot_coding.cds.nr SAMPLES=misc_tests/schizo_ref.samples.txt