I have this version of makefile
[sbsuser#compute-00-01 415]$ make --version GNU Make 3.81
I have directory SOMATIC where I have 3 file . I want to produce a only one output. This is what I wrote.
`
OUTSOMATIC=SOMATIC
FINAL=FINAL
INPUT=$(wildcard $(OUTSOMATIC)/*.vcf)
OUTSORT2= $(patsubst $(OUTSOMATIC)/%.vcf,$(FINAL)/%somatic.ensemble.gz,$(INPUT))
$(info lista $(OUTSORT2))
$(info lista $(INPUT))
.PHONY: all
all: $(INPUT) $(OUTSOMATIC) $(OUTSORT2) $(FINAL)
$(FINAL)/%somatic.ensemble.gz: $(OUTSOMATIC)/%.vcf $(INPUT)
~/jdk1.8.0_121/bin/java -XX:+UseSerialGC -Xms1g -Xmx10g -jar /illumina/software/PROG2/bcbio-variation-recall-0.1.7 ensemble -n 1 $(FINAL)/somatic_ensemble.gz /illumina/software/database/database_2016/hg19_primary.fa $^
`
With this script make 3 time the same files. I don't understand how to create only one output from list of input to use in the same time.
What is the best way to do this?
If I change $(FINAL)/%somatic.ensemble.gz: in $(FINAL)/somatic.ensemble.gz I have this error:
make: *** No rule to make target FINAL/415_merge_mutect2.somaticsomatic.ensemble.gz', needed byall'. Stop`
You probably should review the GNU make manual introductory sections where they describe how make works.
Let's look at your makefile; first you define some variables. Let's assume that you have the files SOMATIC/foo.vcf, SOMATIC/bar.vcf, and SOMATIC/baz.vcf. Then the variables you created will have these values, after they are expanded:
OUTSOMATIC = SOMATIC
FINAL = FINAL
INPUT = SOMATIC/foo.vcf SOMATIC/bar.vcf SOMATIC/baz.vcf
Now your patsubst finds all words in INPUT that match the pattern SOMATIC/%.vcf and replace that with FINAL/%somatic.ensemble.gz, where the part that matches the % in the input is substituted into the output:
OUTSORT2 = FINAL/foosomatic.ensemble.gz FINAL/barsomatic.ensemble.gz FINAL/bazsomatic.ensemble.gz
Now, make sees that you've defined an all target. Since it's the first target in the makefile this is the target that will be run by default. After expansion, it will look like this:
all: SOMATIC/foo.vcf SOMATIC/bar.vcf SOMATIC/baz.vcf SOMATIC FINAL/foosomatic.ensemble.gz FINAL/barsomatic.ensemble.gz FINAL/bazsomatic.ensemble.gz FINAL
So, make will try to build every prerequisite of the all target to be sure it's up to date. First it tries to build the SOMATIC/*.vcf files. Those files already exist and make doesn't have any rules about how to rebuild them, so it assumes they're up to date.
Next it tries to build the SOMATIC file. This is a directory and it also has no rule to be built, so make assumes that's up to date as well.
Next make tries to build the target FINAL/foosomatic.ensemble.gz. Make does have a rule that can build it, you've created one:
$(FINAL)/%somatic.ensemble.gz: $(OUTSOMATIC)/%.vcf $(INPUT)
~/jdk1.8.0_121/bin/java ...
This matches the target you want to build, with a % value of foo, so then make substitutes the % in the prerequisite for foo and finds that SOMATIC/foo.vcf exists and doesn't need to be rebuilt, so it runs your recipe. However your recipe doesn't actually create the target FINAL/foosomatic.ensemble.gz; it creates the target FINAL/somatic_ensemble.gz. So this rule is broken because it tells make it will do one thing, but it does something else.
You should always ensure all your recipes build the file represented by the automatic variable $#; that will ensure that you and make agree on the meaning of your rule. If you want your recipe to build some other file, then your rule is written incorrectly.
Next make does the same thing with the next prerequisite of all: FINAL/barsomatic.ensemble.gz. Since that file doesn't exist, make tries to build it using the pattern rule, but again that creates the same output file.
And again for the third .gz file FINAL/bazsomatic.ensemble.gz. That's why things are run three times.
If you change the pattern rule to an explicit rule building FINAL/somatic.ensemble.gz, which is what you want, then make can't find any way to build the prerequisites of the all target so it gives this error.
Your problem is the creation of OUTSORT2. You want to create only one output file, but you've set OUTSORT2 to contain three different files, so make tries to create all three files. You want this:
OUTSOMATIC = SOMATIC
FINAL = FINAL
INPUT = $(wildcard $(OUTSOMATIC)/*.vcf)
OUTSORT2 = $(FINAL)/somatic.ensemble.gz
.PHONY: all
all: $(OUTSORT2)
$(OUTSORT2): $(INPUT)
~/jdk1.8.0_121/bin/java -XX:+UseSerialGC -Xms1g -Xmx10g -jar /illumina/software/PROG2/bcbio-variation-recall-0.1.7 ensemble -n 1 $# /illumina/software/database/database_2016/hg19_primary.fa $^
Related
Using GNU make, I am trying to solve a problem similar to make recipe execute twice — that is, to have a Makefile recipe run twice. In my case, however, the recipe is run under the .SECONDEXPANSION target, and the two different runs will be called with different parameters to generate different versions of the output file from the same input file. That is, with input file foo, this example Makefile should be callable via make foo.pdf or make foo.expanded.pdf to build one .pdf file, or make all to build both .pdf files:
.PHONY: all
all: foo.pdf foo.expanded.pdf
.SECONDEXPANSION:
%.expanded.pdf %.pdf: %
#echo building $(basename $#)
Of the two solutions given in that answer, the first is unsuitable because it always runs the rule twice; I want it run twice when the user asks for it.
The second solution posted there is conceptually what I am looking for and have implemented in the above example Makefile, with only the small problem that it doesn't work: although the all target lists both .pdf files as dependencies, only one is built when make all is run.
Is there a way to tell GNU make to build two different files using the same rule under a .SECONDEXPANSION?
EDIT: Clarified in problem description that the same input file is used to build both versions of the output file, and modified sample Makefile to include this dependency.
EDIT: I would like a solution as scalable as possible; that is, it should work if the input filename contains dots, specifying additional output file foo.reduced.pdf should require only adjusting the targets and recipe as appropriate, etc. This limits performing string surgery that relies on the filenames appearing exactly as given in this narrow example (e.g., changing the rule to %.pdf: $$(firstword $$(subst ., ,$$*)) fails if the input file could be either foo or foo.bar).
You are probably looking for Pattern-specific Variable Values. Let's assume your recipe depends on a make variable named BUILDFLAGS that takes value normal by default and special for the "expanded" targets. Then this Makefile:
BUILDER := builder
BUILDFLAGS := normal
.PHONY: all
all: foo.pdf foo.expanded.pdf
%.expanded.pdf: BUILDFLAGS := special
%.pdf:
$(BUILDER) $(BUILDFLAGS) $#
should do about what you want with the same rule for all targets, plus one pattern-specific variable value declaration. Replace builder, normal and special with what makes sense in your case. Demo:
$ make foo.pdf
builder normal foo.pdf
$ make foo.expanded.pdf
builder special foo.expanded.pdf
$ make
builder normal foo.pdf
builder special foo.expanded.pdf
Your problem has nothing to do with .SECONDEXPANSION. You can just drop that and the problem will be the same.
Your problem is that you are using a pattern rule with multiple target patterns, and expecting that it works similar to an explicit rule with multiple targets. But it does not (and in fact you cannot have a rule with both pattern and explicit targets).
For a pattern rule with multiple target patterns, Make matches the same pattern to all the %, including multiple times in the targets, and then assumes that it just has to execute the recipe with that pattern once, and it will make all the matched targets.
In your case the best way is to use multiple rules (I changed your recipe because using echo as a Make recipe is a bad idea):
.PHONY: all
all: foo.expanded.pdf foo.pdf
RECIPE = touch $#
%.expanded.pdf:
$(RECIPE)
%.pdf:
$(RECIPE)
I have a very bizzare problem with GNU make. I have the following files:
a/x.html
b/Makefile
b/c/Makefile
The contents of a/x.html are irrelevant. The contents of b/Makefile are as follows:
SRC=../a
all: x.html
%.html: ${SRC}/%.html
rsync $< $#
The contents of b/c/Makefile are the same, except for the definition of SRC:
SRC=../../a
If I run make in b/c/ the result is as expected:
rsync ../../a/x.html x.html
and x.html gets copied from a/ to b/c/.
However, if I run make in b/ the output I get is several lines of:
make: stat: ../a/../a/.. (repeated many times) ../a/x.html: File name too long
It seems that make is applying the rule for %.html recursively, but why? Is there something obvious I am missing?
To build a target that matches the pattern %.html (i.e. any target name that ends in .html), make applies the rule if it can build the dependency (target built from the original target with ../a/ prepended).
You ask to build x.html. This matches the pattern %.html, so the rule applies: make sees if it can build ../a/x.html.
../a/x.html matches the pattern %.html, so the rule applies: make sees if it can build ../a/../a/x.html.
../../a/x.html matches the pattern %.html, so the rule applies, etc.
The stem character can match any part of a path, including directory separators.
You can see what make is trying by running make -r -d (-d to show debugging output, -r to turn off built-in rules which would cause a huge amount of noise).
When you're in b/c, this stops at step 2 because ../../a/x.html exists but ../../../../a/x.html doesn't.
One way to fix this is to list the files on which you want to act. You can build that list from the list of files that already exist in ../a:
$(notdir $(wildcard ${SRC}/*.html)): %.html: ${SRC}/%.html
rsync $< $#
This has the downside that if the HTML files in ../a are themselves built by a rule in b/Makefile, then running make in b won't built them in a pristine source directory. This shouldn't be a problem though: it would be unusual to have a makefile in b build things outside b.
Another approach which doesn't have this defect is to use an absolute path.
%.html: $(abspath ${SRC})/%.html
rsync $< $#
I have another make-like tool that produces an XML as an artifact after parsing my makefile which I'll then further process with Python.
It'd simplify things for me - a lot - if I could have make consider every single prerequisite to be an actual target because then this other tool
will classify each and every file as a "job".
This is a fragment of my makefile:
.obj/eventlookupmodel.o: C:/Users/User1/Desktop/A/PROJ/src/AL2HMIBridge/LookupModels/eventlookupmodel.cpp C:\Users\User1\Desktop\A\PROJ\src\AL2HMIBridge\LookupModels\eventlookupmodel.h \
C:/Users/User1/Desktop/A/PROJ/qt5binaries/include/QtCore/qabstractitemmodel.h \
C:/Users/User1/Desktop/A/PROJ/qt5binaries/include/QtCore/qvariant.h \
...
I'd want for make to think I have a dummy rule for each prerequisite such as below:
C:/Users/User1/Desktop/A/PROJ/qt5binaries/include/QtCore/qvariant.h:
#echo target pre= $#
C:/Users/User1/Desktop/A/PROJ/qt5binaries/include/QtCore/qabstractitemmodel.h:
#echo target pre=$#
C:/Users/User1/Desktop/A/PROJ/src/AL2HMIBridge/LookupModels/eventlookupmodel.cpp :
#echo target pre=$#
C:\Users\User1\Desktop\A\PROJ\src\AL2HMIBridge\LookupModels\eventlookupmodel.h:
#echo target pre=$#
I don't care about the exact form of the rule just that each file is considered an actual target.
My method of passing in this rule would be by setting the MAKEFILES variable like so
make all MAKEFILES=Dummy.mk
with Dummy.mk containing this rule so that I do not modify the makefiles.
I've tried the following so far.
Dummy.mk:
%.h:
#echo header xyz = $#
%:
#echo other xyz= $#
This partially works.
I run make all --trace --print-data-base MAKEFILES=Dummy.mk and I can see that
make does "bind" the %.h: rule to the header files. In the --print-data-base section, I see that rule being assigned to the header files.
C:/Users/User1/Desktop/A/QNX_SDK/target/qnx6/usr/include/stddef.h:
# Implicit rule search has been done.
# Implicit/static pattern stem: 'C:/Users/User1/Desktop/A/QNX_SDK/target/qnx6/usr/include/stddef'
# Last modified 2016-05-27 12:39:16
# File has been updated.
# Successfully updated.
# recipe to execute (from '#$(QMAKE) top_builddir=C:/Users/User1/Desktop/A/HMI_FORGF/src/../lib/armle-v7/release/ top_srcdir=C:/Users/User1/Desktop/A/HMI_FORGF/ -Wall CONFIG+=release CONFIG+=qnx_build_release_with_symbols CONFIG+=rtc_build -o Makefile C:/Users/User1/Desktop/A/HMI_FORGF/src/HmiLogging/HmiLogging.pro
', line 2):
#echo header xyz = $#
However, I do NOT see the "echo header xyz $#"-rule being executed.
Regarding the %: rule, it is neither executed for the .cpp files nor "bound" to them in the --print-data-base section.
However, it is bound and executed for existing targets which have no suffix i.e.
all: library binary
binary: | library
ifs: | library
For the %: rule, the reason for this behavior is because of 10.5.5 Match-Anything Pattern Rules: If you do not mark the match-anything rule as terminal, then it is non-terminal. A non-terminal match-anything rule cannot apply to a file name that indicates a specific type of data. A file name indicates a specific type of data if some non-match-anything implicit rule target matches it.
If I make it non-terminal - no double colon - then the rule doesn't apply to built-in types like .cppunless I un-define the built-in rules that negate my intended %: rule.
If I make it terminal, "it does not apply unless its prerequisites actually exist". But a .h or .cpp doesn't technically have prerequisites; can I just create a dummy file and have that as its prerequisite?
NOTE: This has NOTHING to do with gcc -M generation. Yes the -M option would help in the specific case of header and source files but this question is for more generic targets and prerequisites that already exist in the makefile when make is launched.
This may take a few iterations. Try:
%.h: null
#echo header xyz = $#
%: null
#echo other xyz= $#
null:
#:
Try generating static pattern rules for the header files. See one of the answers to Make ignoring Prerequisite that doesn't exist.
Static pattern rules only apply to an explicit list of target files like this:
$(OBJECTS): %.o: %.c
*recipe here*
where the variable OBJECTS is defined earlier in the makefile to be a list of target files (separated by spaces), for example:
OBJECTS := src/fileA.c src/fileB.c src/fileC.c
Note that you can use the various make utility functions to build that list of target files. For example, $(wildcard pattern), $(addsuffix), etc.
You should also ensure that the recipe "touches" the header file to change the timestamp.
I've found that using static pattern rules instead of pattern rules fixes problems where make doesn’t build prerequisites that don’t exist, or deletes files that you want.
Here is an example of using wildcard to copy files from one directory to another.
# Copy images to build/images
img_files := $(wildcard src/images/*.png src/images/*.gif src/images/*.jpg \
src/images/*.mp3)
build_images := $(subst src/,$(BUILD_DIR)/,$(img_files))
$(build_images): $(BUILD_DIR)/images/% : src/images/%
mkdir -p $(dir $#)
cp -v -a $< $#
There are other make functions like addprefix that could be used to generate a more complex file specification.
I am trying to compile an OpenCobol program using make. I am always getting "make: Nothing to be done for test1.cob". Here is my makefile. I had put a TAB before cobc. But still I am getting that message. Please help.
Thanks.
COBCWARN = -W
%: %.cob
cobc $(COBCWARN) -free -x $^ -o $#
And here is my cobol program.
IDENTIFICATION DIVISION.
PROGRAM-ID. TEST1.
PROCEDURE DIVISION.
DISPLAY 'Hello world!'.
STOP RUN.
Your makefile contains no actual targets. You have defined only a pattern rule which tells make how to build targets that match the pattern. But make doesn't go looking for targets out on the filesystem that could match the pattern, it only checks the pattern against targets that have been specifically requested.
You don't have any specific targets (files) listed in your makefile, so the only way make can know about a target is if you give the target to be built on the command line.
You are running this command from within vim, using the % special token, which expands to the name of the file currently being edited. That means you are running the command:
make test1.cob
because you are editing the file test1.cob. So, you are telling make "please try to create the target (file) test1.cob". But, that file already exists (it's the file you're writing). So make says "nothing to do".
If you run make and ask it to create the target you really want created, it will work:
make test1
Now the file test1 doesn't exist, and make can find a pattern rule that knows how to build it, so make will run that rule.
Alternatively, you can edit your makefile to add the specific target, like this:
COBCWARN = -W
test1: test1.cob
%: %.cob
cobc $(COBCWARN) -free -x $^ -o $#
Then you can run make with no arguments at all. Without any command line arguments, make will look in the makefile for explicit targets and find test1 as the first one. It sees that there is a rule (the pattern rule) that matches that target, so it will build that target.
UPDATE
If you want to allow a simple command make to build multiple programs, write your makefile like this:
COBCWARN = -W
all: test1 test2 test3
.PHONY: all
%: %.cob
cobc $(COBCWARN) -free -x $^ -o $#
Now from vim you can just say :!make and that's it.
If you run make with no arguments then it will find the first explicit target in the makefile and build that. In this example the first target is all, and its prerequisites are the possible programs to build. To build each one make sees that it can apply the pattern rule, and so it will do so (if the .cob file has been modified since the last time the program was built).
Assume I have a make rule:
.PHONY:gen
gen: auto.template
generate-sources auto.template
that creates a bunch of files, for example auto1.src, auto2.src, auto3.src and so on.
If I now have rules to build targets from *.src files, like this:
$(patsubst %.src,%.target,$(wildcard *.src)): %.target: %.src
build $< > $#
How can I tell make to first execute the gen rule and then expand the preconditions for the second rule template? GNU extensions are welcome.
Note: I would like to keep it in one make invocation; A trivial solution to this would be to put the second rule in a secondary Makefile.secondrun and call $(MAKE) -f Makefile.secondrun after gen was processed. But I was wondering if there is a better option.
Building off Beta's answer, here's how you can do it using makefile remaking in GNU make, which is not the same thing as recursive make. Rather, it updates an included makefile using a rule in the main makefile, then restarts the original make instance. This is how *.d dependency files are typically generated and used.
# Get the list of auto-generated sources. If this file doesn't exist, or if it is older
# than auto.template, it will get built using the rule defined below, according to the
# standard behavior of GNU make. If autosrcs.mk is rebuilt, GNU make will automatically
# restart itself after autosrcs.mk is updated.
include autosrcs.mk
# Once we have the list of auto-generated sources, getting the list of targets to build
# from them is a simple pattern substitution.
TARGETS=$(patsubst %.src,%.target,$(AUTO_SRCS))
all: $(TARGETS)
# Rule describing how to build autosrcs.mk. This generates the sources, then computes
# the list of autogenerated sources and writes that to autosrcs.mk in the form of a
# make variable. Note that we use *shell* constructs to get the list of sources, not
# make constructs like $(wildcard), which could be expanded at the wrong time relative
# to when the source files are actually created.
autosrcs.mk: auto.template
./generate-sources auto.template
echo "AUTO_SRCS=`echo *.src`" > autosrcs.mk
# How to build *.target files from *.src files.
%.target: %.src
#echo 'build $< > $#'
Short answer: you can't. Make determines all of the rules it will have to execute before it executes any rule.
Longer answer: maybe you can. As you say, you can use recursive Make explicitly, or surreptitiously by, say, building a file which your makefile will include (I'm looking at you, Jack Kelly). Or if you could somehow obtain a list of the files which gen will build, you could write a rule around that. Or you could take a leap of faith like this:
%.target: %.src
build $< > $#
%.src: gen;