diff --git a/test_SuperTranscript/Makefile b/test_SuperTranscript/Makefile
index 2489759..0650675 100644
--- a/test_SuperTranscript/Makefile
+++ b/test_SuperTranscript/Makefile
@@ -1,9 +1,9 @@
 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
 
diff --git a/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_denovo.sh b/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_denovo.sh
index a8b3b90..5e83bd1 100644
--- a/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_denovo.sh
+++ b/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_denovo.sh
@@ -1 +1,2 @@
-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
diff --git a/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_ref.sh b/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_ref.sh
index 2130fd2..002c324 100644
--- a/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_ref.sh
+++ b/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_ref.sh
@@ -1 +1,2 @@
-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
diff --git a/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_denovo.sh b/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_denovo.sh
index 159a1bb..cce8745 100644
--- a/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_denovo.sh
+++ b/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_denovo.sh
@@ -1 +1,2 @@
-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
diff --git a/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_ref.sh b/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_ref.sh
index 8924f25..920a700 100644
--- a/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_ref.sh
+++ b/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_ref.sh
@@ -1 +1,2 @@
-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
diff --git a/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_denovo.sh b/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_denovo.sh
index cc6e694..847f960 100644
--- a/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_denovo.sh
+++ b/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_denovo.sh
@@ -1 +1,2 @@
-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
diff --git a/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_ref.sh b/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_ref.sh
index 1de64f7..acbee67 100644
--- a/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_ref.sh
+++ b/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_ref.sh
@@ -1 +1,2 @@
-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
diff --git a/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_denovo.sh b/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_denovo.sh
index 984a8e5..ac8d75e 100644
--- a/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_denovo.sh
+++ b/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_denovo.sh
@@ -1 +1,2 @@
-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
diff --git a/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_ref.sh b/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_ref.sh
index 2130fd2..002c324 100644
--- a/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_ref.sh
+++ b/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_ref.sh
@@ -1 +1,2 @@
-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
diff --git a/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_denovo.sh b/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_denovo.sh
index c3a2fc1..822a167 100644
--- a/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_denovo.sh
+++ b/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_denovo.sh
@@ -1 +1,2 @@
-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
diff --git a/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_ref.sh b/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_ref.sh
index 8924f25..920a700 100644
--- a/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_ref.sh
+++ b/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_ref.sh
@@ -1 +1,2 @@
-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
diff --git a/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_denovo.sh b/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_denovo.sh
index ebef2e4..23eda78 100644
--- a/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_denovo.sh
+++ b/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_denovo.sh
@@ -1 +1,2 @@
-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
diff --git a/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_ref.sh b/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_ref.sh
index 1de64f7..acbee67 100644
--- a/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_ref.sh
+++ b/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_ref.sh
@@ -1 +1,2 @@
-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